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The transposed DNA libraries were amplified by PCR for 12 cycles and isolated by Ampure XP beads." } ], "disease": [ { "text": "normal", "ontologyTerms": [ "http://purl.obolibrary.org/obo/PATO_0000461" ], "tag": "attribute" } ], "individual": [ { "text": "8013", "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ], "tag": "attribute" } ], "replicate": [ { "text": "rep2", "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "title": [ { "text": "BMP2_6" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA4699332", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2019-03-30T05:06:47.657Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA4699332" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA4699332{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA4699332/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA4699332/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA4699332" } } }, { "name": "E-MTAB-6931:Het1A-HNF4A_2d_rep2", "accession": "SAMEA4753714", "sraAccession": "ERS2573813", "webinSubmissionAccountId": "Webin-24", "taxId": 9606, "status": "PUBLIC", "release": "2018-08-30T17:02:49Z", "update": "2024-02-06T15:46:25.470Z", "submitted": "2018-06-22T14:00:08Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2018-08-30T17:02:49Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2018-06-22T14:00:08Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA4753714", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "UOM" } ], "INSDC first public": [ { "text": "2018-08-30T17:02:49Z" } ], "INSDC last update": [ { "text": "2018-06-22T14:00:08Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS2573813" } ], "Submitter Id": [ { "text": "E-MTAB-6931:Het1A-HNF4A_2d_rep2", "tag": "Namespace:UOM" } ], "broker name": [ { "text": "ArrayExpress", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0009737" ] } ], "cell line": [ { "text": "Het1A", "tag": "attribute" } ], "cell type": [ { "text": "epithelial cell", "ontologyTerms": [ "http://purl.obolibrary.org/obo/CL_0000066" ], "tag": "attribute" } ], "common name": [ { "text": "human", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ] } ], "description": [ { "text": "Protocols: The cells were generated by infecting cells with 2nd generation lentiviruses. The genes are under Tet-on control. 2d and 4d indicates either doxycycline induction for 2 or 4 days. Het1A, Het1A-HNF4A and Het1A-GATA6 cells were cultured in DMEM (+10% FBS and 1% PenStrep) with 100ng/mL doxycycline for 2 or 4 days. Cells were trypsinised and counted. 50000 cells were taken forward for Tn5 reaction. 50000 cells were lysed in ATAC lysis buffer and Tn5 reactions were performed as described in Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. 2013. Jason D. Buenrostro, Paul G. Giresi, Lisa C. Zaba, Howard Y. Chang and William J. Greenleaf. doi:10.1038/nmeth.2688 Libraries were constructed by amplifying transposed DNA with Illumina Nextera adapters." } ], "disease": [ { "text": "normal", "ontologyTerms": [ "http://purl.obolibrary.org/obo/PATO_0000461" ], "tag": "attribute" } ], "genotype": [ { "text": "HNF4A-tet-on", "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ], "tag": "attribute" } ], "organism part": [ { "text": "esophagus", "ontologyTerms": [ "http://purl.obolibrary.org/obo/UBERON_0001043" ], "tag": "attribute" } ], "phenotype": [ { "text": "doxycyclin mediated overexpression of HNF4A", "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "title": [ { "text": "Het1A-HNF4A_2d_rep2" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA4753714", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2019-03-30T05:11:40.631Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA4753714" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA4753714{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA4753714/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA4753714/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA4753714" } } }, { "name": "4c6c80f6-7610-11e8-b8fa-68b59976a384", "accession": "SAMEA4757620", "sraAccession": "ERS2577714", "webinSubmissionAccountId": "Webin-2", "taxId": 9606, "status": "PUBLIC", "release": "2019-09-10T17:03:53Z", "update": "2024-02-06T15:48:17.516Z", "submitted": "2018-06-25T14:39:38Z", "characteristics": { "ArrayExpress-PHENOTYPE": [ { "text": "wildtype", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0005543" ], "tag": "attribute" } ], "ArrayExpress-SPECIES": [ { "text": "Homo sapiens", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ], "tag": "attribute" } ], "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2019-09-10T17:03:53Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2018-06-25T14:39:38Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA4757620", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "SC" } ], "INSDC first public": [ { "text": "2019-09-10T17:03:53Z" } ], "INSDC last update": [ { "text": "2018-06-25T14:39:38Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS2577714" } ], "Submitter Id": [ { "text": "4c6c80f6-7610-11e8-b8fa-68b59976a384", "tag": "Namespace:SC" } ], "common name": [ { "text": "human", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ] } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "phenotype": [ { "text": "wildtype", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0005543" ], "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "subject id": [ { "text": "Th2_ATAC7549204", "tag": "attribute" } ], "title": [ { "text": "C1_Jurkat_110" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA4757620", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2019-09-11T02:49:46.356Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA4757620" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA4757620{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA4757620/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA4757620/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA4757620" } } }, { "name": "E-MTAB-7035:L3.6pl_ATAC_C1", "accession": "SAMEA4799825", "sraAccession": "ERS2619743", "webinSubmissionAccountId": "Webin-24", "taxId": 9606, "status": "PUBLIC", "release": "2018-12-18T17:02:52Z", "update": "2024-02-06T16:07:41.664Z", "submitted": "2018-07-20T14:53:24Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2018-12-18T17:02:52Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2018-07-20T14:53:24Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA4799825", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "Section of Tumor Epigenetics, Department of General, Visceral and Pediatric Surgery, University Medical Center Gottingen, 37075 Gottingen, Germany" } ], "INSDC first public": [ { "text": "2018-12-18T17:02:52Z" } ], "INSDC last update": [ { "text": "2018-07-20T14:53:24Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS2619743" } ], "Submitter Id": [ { "text": "E-MTAB-7035:L3.6pl_ATAC_C1", "tag": "Namespace:Section of Tumor Epigenetics, Department of General, Visceral and Pediatric Surgery, University Medical Center Gottingen, 37075 Gottingen, Germany" } ], "broker name": [ { "text": "ArrayExpress", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0009737" ] } ], "cell line": [ { "text": "L3.6pl", "tag": "attribute" } ], "cell type": [ { "text": "epithelial cell", "ontologyTerms": [ "http://purl.obolibrary.org/obo/CL_0000066" ], "tag": "attribute" } ], "common name": [ { "text": "human", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ] } ], "description": [ { "text": "Protocols: ATAC was performed following the protocol of Buenrostro et al. Briefly, 50,000 L3.6pl cells were trypsinized and washed twice with cold PBS. Then cells were re-suspended in lysis buffer (10mM Tris-HCl pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630) and incubated for 15 minutes at a rotating wheel at 4ºC followed by centrifugation and in re-suspended in 50 µl of transposition mix composed of 2.5µl of TDE1 (Nextera Tn5 Transposase), 25 µl TD (2x reaction buffer) in nuclease free water (Nextera DNA Library Prep Kit, FC-121-1030, Illumina). Then it was incubated at 37 degrees for 30 minutes. MinElute PCR Purification kit (Qiagen) was used for DNA extraction following the instructions of the manufacturer. ATAC libraries were made using the Nextera DNA Library Prep Kit according to Buenrostro et al. The libraries were amplified for 15 cycles in total of: 98ºC for 10 seconds, 63ºC for 30 seconds, and 72ºC for 60 seconds." } ], "disease": [ { "text": "pancreatic adenosquamous carcinoma", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0006732" ], "tag": "attribute" } ], "metastatic site": [ { "text": "celiac lymph node", "ontologyTerms": [ "http://purl.obolibrary.org/obo/UBERON_0002508" ], "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ], "tag": "attribute" } ], "organism part": [ { "text": "pancreas", "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "title": [ { "text": "L3.6pl_ATAC_C1" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA4799825", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2019-03-30T05:21:04.355Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA4799825" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA4799825{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA4799825/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA4799825/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA4799825" } } }, { "name": "E-MTAB-67141538733896:plate_K562_rep2_71", "accession": "SAMEA4955936", "sraAccession": "ERS2774518", "webinSubmissionAccountId": "Webin-24", "taxId": 9606, "status": "PUBLIC", "release": "2018-10-10T17:03:13Z", "update": "2024-02-06T17:05:56.732Z", "submitted": "2018-10-05T11:29:33Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2018-10-10T17:03:13Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2018-10-05T11:29:33Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA4955936", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "WELLCOME TRUST SANGER INSTITUTE" } ], "INSDC first public": [ { "text": "2018-10-10T17:03:13Z" } ], "INSDC last update": [ { "text": "2018-10-05T11:29:33Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS2774518" } ], "Submitter Id": [ { "text": "E-MTAB-67141538733896:plate_K562_rep2_71", "tag": "Namespace:WELLCOME TRUST SANGER INSTITUTE" } ], "broker name": [ { "text": "ArrayExpress", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0009737" ] } ], "cell line": [ { "text": "K562", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0002067" ], "tag": "attribute" } ], "cell type": [ { "text": "lymphoblast", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0000572" ], "tag": "attribute" } ], "common name": [ { "text": "human", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ] } ], "description": [ { "text": "Protocols: The spleen from a C57BL/6Jax mouse was mashed by a 2-ml syringe plunger through a 70 μm cell strainer (Fisher Scientific 10788201) into 30 ml 1X DPBS (ThermoFisher 14190169) supplied with 2 mM EDTA and 0.5% (w/v) BSA (Sigma A9418). Cells were centrifuged down, supernatant was removed, and the cell pellet was briefly vortexed. 5 ml 1X RBC lysis buffer (ThermoFisher 00-4300-54) was used to resuspend the cell pellet, and the cell suspension was vortexed again, and left on bench for 5 minutes to lyse red blood cells. Then 45 ml 1X DPBS was added, and cells were centrifuged down. 30 ml 1X DPBS were used to resuspend the cell pellet. The cell suspension was passed through a Miltenyi 30 μm Pre-Separation Filter (Miltenyi 130-041-407), and the cell number was determined using C-chip counting chamber (VWR DHC-N01). All centrifugations were done at 500 g, 4 °C, 5 minutes. After tagmentation, DAPI was added at a final concentration of 1 ug/ml. Then DAPI positive nuclei were sorted into 384-well plate using BD-INFLUX sorter. The nuclei sorting was performed at the Flow Cytometry facility at the Wellcome Trust Sanger Institute. Nuclei prepration and ATAC-seq procedure are performed simultaneously, i.e. Fast-ATAC protocol was used (Corces et al. Nature Genetics, 48, 1193-1203, 2016). Briefly, 50,000 cells were pelleted down at 500 g, 4 degree for 5 minutes. Then cell pellet was resuspended in 50 ul tagmentation mix containing 33 mM Tris-acetate, pH7.8, 66 mM potassium acetate, 10 mM magnesium acetate, 16% (v/v) dimethylformamide, 0.01% digitonin, 5 ul Tn5 transposes (Nextera kit, Illumina Cat No. FC-121-1030). The tagmentation reaction was put on a thermomixer, with 37 degree for 30 minutes. Then reaction was stopped by adding 50 ul 20 mM EDTA pH 8.0. After tagmentation, DAPI was added at a final concentration of 1 ug/ml. Then DAPI positive nuclei were sorted into 384-well plate using BD-INFLUX sorter. The nuclei sorting was performed at the Flow Cytometry facility at the Wellcome Trust Sanger Institute. DNA was purified first by Qiagen minElute PCR purification kit according to the manufacturer's instruction, then by AmupureXP beads with 0.5X upper cutoff and a 1.2X lower cutoff according to manufacturer's instruction. Libraries were constructed in the Illumina Nextera DNA Library preparation kit." } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ], "tag": "attribute" } ], "organism part": [ { "text": "bone marrow", "tag": "attribute" } ], "post analysis well quality": [ { "text": "pass", "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "sex": [ { "text": "female", "ontologyTerms": [ "http://purl.obolibrary.org/obo/PATO_0000383" ], "tag": "attribute" } ], "title": [ { "text": "plate_K562_rep2_71" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA4955936", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2019-03-30T05:44:05.808Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA4955936" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA4955936{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA4955936/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA4955936/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA4955936" } } }, { "name": "E-MTAB-7543:Sample 3", "accession": "SAMEA5187676", "sraAccession": "ERS2995173", "webinSubmissionAccountId": "Webin-24", "taxId": 9606, "status": "PUBLIC", "release": "2019-02-28T17:01:57Z", "update": "2024-02-06T18:16:40.006Z", "submitted": "2018-12-18T16:11:39Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2019-02-28T17:01:57Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2018-12-18T16:11:39Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA5187676", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "The Children's Hospital of Philadelphia" } ], "INSDC first public": [ { "text": "2019-02-28T17:01:57Z" } ], "INSDC last update": [ { "text": "2018-12-18T16:11:39Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS2995173" } ], "Submitter Id": [ { "text": "E-MTAB-7543:Sample 3", "tag": "Namespace:The Children's Hospital of Philadelphia" } ], "broker name": [ { "text": "ArrayExpress", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0009737" ] } ], "cell line": [ { "text": "HepG2", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0001187" ], "tag": "attribute" } ], "cell type": [ { "text": "epithelial cell", "ontologyTerms": [ "http://purl.obolibrary.org/obo/CL_0000066" ], "tag": "attribute" } ], "common name": [ { "text": "human", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ] } ], "description": [ { "text": "Protocols: Cells were harvested via trypsinization, followed by a series of wash steps. 100,000 cells of each were spun down at 550xg for 5min, 4C. Supernatant was removed; 50uL of PBS was added to wash pellet. Spin conditions remained the same. The cell pellet was resuspended in 50ul cold lysis buffer (1 mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630), spun down immediately at 550xg for 10min, 4C. The nuclei resuspended in the transposition reaction mix (2x TD Buffer (Illumina Cat #FC-121-1030, Nextera), 2.5ul Tn5 Transposes (Illumina Cat #FC-121-1030, Nextera) and Nuclease Free H2O) on ice. The transposition reaction was incubated at 37C for 45min. The transposed DNA was then purified using a Qiagen MinElute Kit with 10.5ul elution buffer. The transposed library was then PCR amplified using Nextera primers for 12 cycles. The PCR reaction was subsequently cleaned up using AMPureXP beads (Agencourt)." } ], "disease": [ { "text": "hepatocellular carcinoma", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0000182" ], "tag": "attribute" } ], "genotype": [ { "text": "wild type genotype", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0005168" ], "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ], "tag": "attribute" } ], "organism part": [ { "text": "liver", "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "title": [ { "text": "Sample 3" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA5187676", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2019-03-30T06:06:45.729Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA5187676" }, "curationDomain": { 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"Namespace:BioSample" } ], "INSDC center name": [ { "text": "KI-BN" } ], "INSDC first public": [ { "text": "2020-04-14T16:27:49Z" } ], "INSDC last update": [ { "text": "2021-06-30T00:26:00Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS3164342" } ], "Submitter Id": [ { "text": "CMT+sgTP53", "tag": "Namespace:KI-BN" } ], "common name": [ { "text": "human", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ] } ], "description": [ { "text": "ATAC-seq from CMT+sgTP53 transformed cells" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "title": [ { "text": "ATAC-seq", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0007045" ] } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA5358722", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2018-12-20T12:33:11.961Z", "_links": { "self": { "href": 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"2019-03-15T10:10:05Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA5424640", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "ERASMUS MC" } ], "INSDC first public": [ { "text": "2020-01-06T04:04:25Z" } ], "INSDC last update": [ { "text": "2019-03-15T10:10:05Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS3229928" } ], "Submitter Id": [ { "text": "KLF1-32_I16-1584-05-m5", "tag": "Namespace:ERASMUS MC" } ], "cell type": [ { "text": "Erythroid progenitors", "ontologyTerms": [ "http://purl.obolibrary.org/obo/CL_0000038" ], "tag": "attribute" } ], "common name": [ { "text": "human", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ] } ], "description": [ { "text": "KLF1 haploinsufficiency m5 48 hrs differentiation erythroblasts ATAC-seq fastq files" } ], "dev stage": [ { "text": "Adult", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0001272" ], "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "tissue type": [ { "text": "Peripheral blood", "ontologyTerms": [ "http://purl.obolibrary.org/obo/UBERON_0000178" ], "tag": "attribute" } ], "title": [ { "text": "KLF1 haploinsufficiency m5 48 hrs differentiation erythroblasts ATAC-seq" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA5424640", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2019-01-29T09:49:08.640Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA5424640" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA5424640{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA5424640/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA5424640/curationlinks/{hash}", "templated": true }, "structuredData": { "href": 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"E-MTAB-7844:789o_2", "tag": "Namespace:Novartis Institutes for Biomedical Research" } ], "broker name": [ { "text": "ArrayExpress", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0009737" ] } ], "cell line": [ { "text": "786-0", "tag": "attribute" } ], "cell type": [ { "text": "epithelial cell", "ontologyTerms": [ "http://purl.obolibrary.org/obo/CL_0000066" ], "tag": "attribute" } ], "common name": [ { "text": "human", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ] } ], "description": [ { "text": "Protocols: 150000 Cells were lysed in ATAC-lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and immediately processed for tagmentation. Tagmentation was performed as described in Buenrostro et al. Curr Protoc. Mol. Biol., 2016 using the Illumina Nextera Tn5 Transposase. ATAC-seq libraries were amplified from the tagmentation reaction by PCR using the PPC (PCR Primer mix) from the Illumina Nextera Tn5 Transposase kit and adding barcodes from the Nextera Index Kit (24 indexes 96 samples). DNA was purified using AmpPure XP beads." } ], "disease": [ { "text": "renal cell carcinoma", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0000681" ], "tag": "attribute" } ], "genotype": [ { "text": "doxycycline inducible PAX8 knockdown", "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ], "tag": "attribute" } ], "organism part": [ { "text": "kidney", "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "title": [ { "text": "789o_2" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA5547873", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2019-06-29T02:22:56.145Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA5547873" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA5547873{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA5547873/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA5547873/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA5547873" } } }, { "name": "E-MTAB-7878:HAEC_ATAC_TNFa_biorep_1", "accession": "SAMEA5568462", "sraAccession": "ERS3370485", "webinSubmissionAccountId": "Webin-24", "taxId": 9606, "status": "PUBLIC", "release": "2020-04-14T16:26:05Z", "update": "2024-02-06T20:50:07.750Z", "submitted": "2019-04-16T11:56:50Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2020-04-14T16:26:05Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2019-04-16T11:56:50Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA5568462", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "The Hospital for Sick Children, Genetics and Genome Biology University of Toronto, Department of Molecular Genetics" } ], "INSDC first public": [ { "text": "2020-04-14T16:26:05Z" } ], "INSDC last update": [ { "text": "2019-04-16T11:56:50Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS3370485" } ], "Submitter Id": [ { "text": "E-MTAB-7878:HAEC_ATAC_TNFa_biorep_1", "tag": "Namespace:The Hospital for Sick Children, Genetics and Genome Biology University of Toronto, Department of Molecular Genetics" } ], "age": [ { "text": "21 years old", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0004340" ], "tag": "attribute" } ], "broker name": [ { "text": "ArrayExpress", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0009737" ] } ], "cell type": [ { "text": "primary human aortic endothelial cell", "ontologyTerms": [ "http://purl.obolibrary.org/obo/CL_0002544" ], "tag": "attribute" } ], "common name": [ { "text": "human", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ] } ], "description": [ { "text": "Protocols: Primary aortic endothelial cells (ECs) isolated from human aorta (HAECs: two 21 year old Caucasian males), mouse aorta (MAECs: two biological replicates of C57BL/6 males from pooled mice), and bovine aorta (BAEC: two biological replicates) were grown in cell culture. Cells were cultured at 37°C and 5% CO2 supplied with Endothelial Cell Growth Media MV2 (PromoCell) supplemented with 5% fetal calf serum (PromoCell), 5 ng/ml recombinant human epidermal growth factor (PromoCell), 0.5 ng/ml recombinant human vascular endothelial growth factor 165 (PromoCell), 10 ng/ml recombinant human basic fibroblast growth factor (PromoCell), 20 ng/ml long R3 insulin-like growth factor-1 (PromoCell), 1 μg/ml ascorbic acid (PromoCell) and 0.2 μg/ml hydrocortisone (PromoCell). All experiments were carried out before passage 9. HAECs were treated with 10 ng/mL recombinant human TNFα (Cell Applications, cat# RP1111-50), MAECs were treated with 10 ng/mL recombinant mouse TNFα (Cell Applications, cat# RP2031-20), and BAECs were treated with 10 ng/mL recombinant bovine TNFα (R&D Systems, cat# 2279-BT-025) for 45 mins in basal Endothelial Cell Growth Media MV2 (PromoCell) without supplements. The un-stimulated control samples were treated with vehicle (water). ~50K cells were harvested from each biological replicate of un-stimulated and TNF-α stimulated (45 min. 10 ng/ml) HAECs (#1487 and #2139), MAECs (#A092913T2MP and #B092913T2MP), and BAECs (#1165 and #1190). Cells were lysed in nonionic detergent lysis buffer (10 mM Tris-HCl, pH 7.4, 3 mM MgCl2, 10 mM NaCl, 0.1% NP-40) for nuclei isolation. The nuclei were pelleted and re-suspended in 50 ul transposition reaction solution of 2.5 ul transposome complex containing Tn5 transposase attached to sequencing adapters (Illumina Nextera Tagment DNA enzyme TDE1, Nextera® DNA Sample Preparation Kit cat# FC-121-1030), 25 ul Illumina Tagment DNA buffer (TD, Nextera® DNA Sample Preparation Kit cat# FC-121-1030), and 22.5 ul of nuclease free water and incubated at 37°C for 30 min under gentle mixing condition (300 rpm). The transposed and adapter-ligated DNA fragments were purified using a Qiagen MinElute PCR Purification Kit The purified DNA was PCR amplified using barcoded primers (Nextera Index Kit, FC-121-1011) for 12 cycles: [72°C for 5 min, 98°C for 30 sec (98°C for 10 sec, 63°C for 30 sec, 72°C for 1 min) x 12]. Agencourt AMPure XP beads (Beckman Coulter) were used for size-selection of >150bp DNA fragments." } ], "individual": [ { "text": "1487", "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ], "tag": "attribute" } ], "organism part": [ { "text": "aorta endothelium", "tag": "attribute" } ], "replicate": [ { "text": "1", "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "sex": [ { "text": "male", "ontologyTerms": [ "http://purl.obolibrary.org/obo/PATO_0000384" ], "tag": "attribute" } ], "stimulus": [ { "text": "tumor necrosis factor-alpha", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0003271" ], "tag": "attribute" } ], "title": [ { "text": "HAEC_ATAC_TNFa_biorep_1" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA5568462", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2019-02-09T12:26:48.248Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA5568462" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA5568462{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA5568462/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA5568462/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA5568462" } } }, { "name": "E-MTAB-8089:Sample 140", "accession": "SAMEA5820310", "sraAccession": "ERS3608901", "webinSubmissionAccountId": "Webin-24", "taxId": 9606, "status": "PUBLIC", "release": "2019-10-16T17:04:27Z", "update": "2024-02-06T22:21:19.473Z", "submitted": "2019-07-31T12:50:32Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2019-10-16T17:04:27Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2019-07-31T12:50:32Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA5820310", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "MPI-EVA" } ], "INSDC first public": [ { "text": "2019-10-16T17:04:27Z" } ], "INSDC last update": [ { "text": "2019-07-31T12:50:32Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS3608901" } ], "Submitter Id": [ { "text": "E-MTAB-8089:Sample 140", "tag": "Namespace:MPI-EVA" } ], "broker name": [ { "text": "ArrayExpress", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0009737" ] } ], "cell line": [ { "text": "mixed 409B2 and H9", "tag": "attribute" } ], "cell type": [ { "text": "mixed embryonic stem cell and induced pluripotent stem cell", "tag": "attribute" } ], "common name": [ { "text": "human", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ] } ], "description": [ { "text": "Protocols: For organoid experiments (2 months, 4 months), organoids were washed twice with PBS in a Tissue-Tek Cryomold (Sakura), then embedded in 4% low-melting agarose (Sigma) and sliced into 150 μm sections using a vibrating microtome (Ci 7000 smz, Camden Instruments). Slices were placed on microscope slides containing differentiation plus vitamin A (Diff +VA) media and inspected under a stereomicroscope (Leica) to dissect cortical regions. Selected regions were washed twice in 500 μL PBS and incubated at 37°C in 500 μL Accutase (Sigma) plus 0.5 μL DNase I (New England Biolabs) for ~45 minutes. Trituration was performed for additional mechanical dissociation. Cells were passed through a 30 μm pre-separation filter (Miltenyi Biotec), washed with Diff+VA medium, and spun down at 300 x g (Heraeus Megafuge 40R, Thermo Scientific) for 5 minutes. The cell pellet was resuspended in 200 μl of Diff+VA medium. Cells were viewed under a microscope (Zeiss) to ensure a single cell suspension was obtained, and then counted using a Countess Automated Cell Counter (Invitrogen). From this cell suspension, cells were diluted to a final concentration of 300 cells/μl and used for microfluidics based single-cell ATAC-seq. All the protocols are the same as in E-MTAB-8083 (ie as described in Lancaster et al. 2014) Cerebral organoids were generated independently for the H9 embryonic stem cell line (from WiCell) and the 409B2 induced pluripotent stem cell line (from the RIKEN BRC cell bank). During the experiments, we took an equal number of H9 organoids and 409B2 organoids, dissociated the organoids into single cells independently for each line, and then obtained a cell count for each line. Finally, we took an equal number of H9 cells and 409B2 cells (1:1 ratio) and loaded this cell mixture into the Fluidigm IFC for capturing and performing the single-cell ATAC-seq protocol. Description and phenotype annotation is as follows: d30: this refers to organoids after 30 days differentiation but no clear cell type; EB: this refers to embryoid bodies prior to organoid differentiation; iPSC: this refers to induced pluripotent stem cells prior to embryoid body or organoid culture; NEcto: this refers to organoids where cells have differentiated to neuroectoderm fate; NEpith: this refers to organoids where cells have differentiated to neuroepithelial fate; organoid: this refers to organoids where no cell fate was determined Cells were mixed with Suspension Reagent (Fludigm) at a 3:2 ratio and loaded onto a primed medium (10-17 μm) integrated microfluidic circuit (Fludigm) for capturing. Lysis, transposition, and amplification were performed on the Fluidigm C1 platform. DNA from each cell was transferred to an individual well of a 96-well plate and barcoded with unique combinations of 24 adapter-index i7 and 16 adapter-index i5 primers. Quantification and library size distribution was assessed on an Agilent 2100 Bioanalyzer using High Sensitivity DNA chips. Excessive primer contamination was removed using SPRIselect (Beckman Coulter Life Sciences) size selection." } ], "developmental stage": [ { "text": "mixed adult and embryo", "tag": "attribute" } ], "disease": [ { "text": "normal", "ontologyTerms": [ "http://purl.obolibrary.org/obo/PATO_0000461" ], "tag": "attribute" } ], "genotype": [ { "text": "wild type genotype", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0005168" ], "tag": "attribute" } ], "growth condition": [ { "text": "organoid culture", "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ], "tag": "attribute" } ], "organism part": [ { "text": "mixed embryo and skin", "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "single cell well quality": [ { "text": "OK", "tag": "attribute" } ], "title": [ { "text": "Sample 140" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA5820310", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2019-10-17T03:16:05.479Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA5820310" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA5820310{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA5820310/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA5820310/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA5820310" } } }, { "name": "E-MTAB-8228:Sample 3", "accession": "SAMEA5857953", "sraAccession": "ERS3646470", "webinSubmissionAccountId": "Webin-24", "taxId": 9606, "status": "PUBLIC", "release": "2019-10-16T17:04:27Z", "update": "2024-02-06T22:41:49.377Z", "submitted": "2019-08-07T14:39:54Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2019-10-16T17:04:27Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2019-08-07T14:39:54Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA5857953", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "MPI-EVA" } ], "INSDC first public": [ { "text": "2019-10-16T17:04:27Z" } ], "INSDC last update": [ { "text": "2019-08-07T14:39:54Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS3646470" } ], "Submitter Id": [ { "text": "E-MTAB-8228:Sample 3", "tag": "Namespace:MPI-EVA" } ], "age": [ { "text": "36", "unit": "year", "tag": "attribute" } ], "broker name": [ { "text": "ArrayExpress", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0009737" ] } ], "cell line": [ { "text": "409B2", "tag": "attribute" } ], "cell type": [ { "text": "induced pluripotent stem cell", "tag": "attribute" } ], "common name": [ { "text": "human", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ] } ], "description": [ { "text": "Protocols: Organoids were washed twice with PBS in a Tissue-Tek Cryomold (Sakura), then embedded in 4% low-melting agarose (Sigma) and sliced into 150 μm sections using a vibrating microtome (Ci 7000 smz, Camden Instruments). Slices were placed on microscope slides containing differentiation plus vitamin A (Diff +VA) media and inspected under a stereomicroscope (Leica) to dissect cortical regions. Selected regions were washed twice in 500 μL PBS and incubated at 37°C in 500 μL Accutase (Sigma) plus 0.5 μL DNase I (New England Biolabs) for ~45 minutes. Trituration was performed for additional mechanical dissociation. Cells were passed through a 30 μm pre-separation filter (Miltenyi Biotec), washed with Diff+VA medium, and spun down at 300 x g (Heraeus Megafuge 40R, Thermo Scientific) for 5 minutes. The cell pellet was resuspended in 200 μl of Diff+VA medium. Cells were viewed under a microscope (Zeiss) to ensure a single cell suspension was obtained, and then counted using a Countess Automated Cell Counter (Invitrogen). From the cell suspension, 50,000 cells were used as input for bulk ATAC-seq (as described in Buenrostro et al. 2013). All stem cell lines were cultured using standard feeder-free conditions in mTeSR1 (StemCell Technologies) on matrigel-coated plates and differentiated into cerebral organoids using a whole organoid differentiation protocol as described in Lancaster et al. 2014. Human cerebral organoids were generated independently for the H9 embryonic stem cell line (from WiCell), and the induced pluripotent stem cell lines 409B2 (from the RIKEN BRC cell bank) and SC102A-1 (from System Biosciences). Chimpanzee cerebral organoids were generated independently for the induced pluripotent stem cell lines SandraA (a 7 year old female chimpanzee from Leipzig Zoo, Germany, when lymphocytes were obtained from her blood, then reprogrammed using plasmid based reprogramming per Okita et al. 2013; non-transgenic cell line), JoC (an 18 year old male chimpanzee from the Tchimpounga Sanctuary when lymphocytes were obtained from his blood, then reprogrammed using plasmid based reprogramming per Okita et al. 2013; non-transgenic cell line) and PR818-5 (originally generated by the Gage lab and kindly provided to us by the R. Livesey group). Bonobo cerebral organoids were generated for the induced pluripotent stem cell line Bokela (an 8 year old female bonobo from Leipzig Zoo, Germany, when fibroblasts were sampled from her skin, then reprogrammed using the StemMACS mRNA transfection kit; non-transgenic cell line). Macaque cerebral organoids were generated for the MN-1 embryonic stem cell line (kindly provided to us by the R. Livesey group who received them from Eliza Curnow). Following the protocol of Buenrostro et al. 2013, 50,000 cells were spun down in a refrigerated centrifuge (4°C) for 5 min at 500xg. The supernatant was removed and cells were washed with 50 uL cold PBS buffer, then spun down for 5 min at 500xg. The supernatant was removed and the cell pellet was resuspended in 50 uL of cold lysis buffer, then centrifuged for 10 min at 500xg. The supernatant was removed, the nuclei pellet was placed on ice, and we immediately proceeded to the transposition reaction. The nuclei pellet was resuspended in 50 uL cold transposition reaction mix (2.5 uL TDE1/Tn5 transposase from the Illumina Nextera kit, 25 uL TD 2x reaction buffer from the Illumina Nextera kit, 22.5 uL nuclease-free water) and incubated at 37°C for 30 minutes in a Thermomixer. The transposed DNA was purified using a QiaGen MinElute PCR Purification Kit. To determine the number of amplification cycles needed, we performed a qPCR side reaction using 100x SYBR Green 1. Transposed DNA from each sample was then amplified and barcoded with unique combinations of 24 adapter-index i7 and 16 adapter-index i5 primers. Quantification and library size distribution was assessed on an Agilent 2100 Bioanalyzer using High Sensitivity DNA chips. Excessive primer contamination was removed using SPRIselect (Beckman Coulter Life Sciences) size selection." } ], "developmental stage": [ { "text": "adult", "tag": "attribute" } ], "disease": [ { "text": "normal", "ontologyTerms": [ "http://purl.obolibrary.org/obo/PATO_0000461" ], "tag": "attribute" } ], "genotype": [ { "text": "wild type genotype", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0005168" ], "tag": "attribute" } ], "growth condition": [ { "text": "organoid culture", "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ], "tag": "attribute" } ], "organism part": [ { "text": "skin", "tag": "attribute" } ], "progenitor cell type": [ { "text": "fibroblast", "ontologyTerms": [ "http://purl.obolibrary.org/obo/CL_0000057" ], "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "sex": [ { "text": "female", "ontologyTerms": [ "http://purl.obolibrary.org/obo/PATO_0000383" ], "tag": "attribute" } ], "title": [ { "text": "Sample 3" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA5857953", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2019-10-17T03:16:08.624Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA5857953" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA5857953{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA5857953/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA5857953/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA5857953" } } }, { "name": "E-MTAB-8264:shZEB1_ATACseq_replicate1", "accession": "SAMEA5877041", "sraAccession": "ERS3665508", "webinSubmissionAccountId": "Webin-24", "taxId": 9606, "status": "PUBLIC", "release": "2020-07-22T08:04:40Z", "update": "2024-02-06T22:52:40.156Z", "submitted": "2019-08-20T15:27:55Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2020-07-22T08:04:40Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2019-08-20T15:27:55Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA5877041", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "Department of Experimental Medicine 1, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-University Erlangen-Nurnberg, Erlangen, Germany" } ], "INSDC first public": [ { "text": "2020-07-22T08:04:40Z" } ], "INSDC last update": [ { "text": "2019-08-20T15:27:55Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS3665508" } ], "Submitter Id": [ { "text": "E-MTAB-8264:shZEB1_ATACseq_replicate1", "tag": "Namespace:Department of Experimental Medicine 1, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-University Erlangen-Nurnberg, Erlangen, Germany" } ], "age": [ { "text": "51", "unit": "year", "tag": "attribute" } ], "broker name": [ { "text": "ArrayExpress", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0009737" ] } ], "cell line": [ { "text": "MDAMB231", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0001209" ], "tag": "attribute" } ], "cell type": [ { "text": "mammary epithelial cell", "ontologyTerms": [ "http://purl.obolibrary.org/obo/CL_0002327" ], "tag": "attribute" } ], "common name": [ { "text": "human", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ] } ], "description": [ { "text": "Protocols: Chromatin accessibility mapping was performed using the ATAC-seq method as described in (Corces, M.R. et al., An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues., Nat Methods, 2017). For the transposition reaction cell nuclei were carefully resuspended in (25 µl 2 x TD buffer (Illumina), 2.5 µl TDE1 (Illumina), 16.5 µl PBS, 5 µl nuclease-free water, 0.5 µl 1% Digitonin (Promega), 0.5 µl 10% Tween-20 (Sigma)) for 30min at 37°C on a shaker at 1000rpm. MDA-MB-231 cells were purchased from the American Type Culture Collection (ATCC) and cultured under standard conditions in DMEM (Gibco) supplemented with 10% fetal bovine serum (Gibco) and 1.0µg/ml puromycin. Stably transduced MDA-MB-231 shCtrl and shZEB1 cell lines were generated as described in (Spaderna, S. et al., The transcriptional repressor ZEB1 promotes metastasis and loss of cell polarity in cancer., Cancer research, 2008). DNA was purified with the Clean and Concentrator-5 kit (Zymo). Library material was amplified using custom Nextera primers and was followed by SPRI size selection with AmpureXP beads to exclude most fragments larger than 1,200bp. DNA concentration was measured with a Qubit fluorometer (Life Technologies)." } ], "developmental stage": [ { "text": "adult", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0001272" ], "tag": "attribute" } ], "disease": [ { "text": "breast adenocarcinoma", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0000304" ], "tag": "attribute" } ], "genotype": [ { "text": "wild type genotype", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0005168" ], "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ], "tag": "attribute" } ], "organism part": [ { "text": "mammary gland", "ontologyTerms": [ "http://purl.obolibrary.org/obo/UBERON_0001911" ], "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "title": [ { "text": "shZEB1_ATACseq_replicate1" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA5877041", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2019-06-13T03:52:06.635Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA5877041" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA5877041{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA5877041/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA5877041/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA5877041" } } }, { "name": "E-MTAB-8447:T_007 rep2", "accession": "SAMEA6087989", "sraAccession": "ERS3888395", "webinSubmissionAccountId": "Webin-24", "taxId": 9606, "status": "PUBLIC", "release": "2020-03-09T04:03:25Z", "update": "2024-02-07T00:26:43.813Z", "submitted": "2019-10-17T09:39:43Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2020-03-09T04:03:25Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2019-10-17T09:39:43Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA6087989", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "UNIVERSITY OF MANCHESTER" } ], "INSDC first public": [ { "text": "2020-03-09T04:03:25Z" } ], "INSDC last update": [ { "text": "2019-10-17T09:39:43Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS3888395" } ], "Submitter Id": [ { "text": "E-MTAB-8447:T_007 rep2", "tag": "Namespace:UNIVERSITY OF MANCHESTER" } ], "age": [ { "text": "not available", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0001071" ], "tag": "attribute" } ], "broker name": [ { "text": "ArrayExpress", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0009737" ] } ], "common name": [ { "text": "human", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ] } ], "description": [ { "text": "Protocols: Biopsies were collected from consenting patients and snap frozen. Biopsies were minced with a scalpel and lysed in ATAC lysis buffer and Tn5 reactions were performed as described in \\An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues\\ Corces et al (2017) https://www.nature.com/articles/nmeth.4396 Libraries were constructed by amplifying transposed DNA with Illumina Nextera adapters as described in \\An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues\\ Corces et al (2017) https://www.nature.com/articles/nmeth.4396" } ], "disease": [ { "text": "esophageal adenocarcinoma", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0000478" ] } ], "individual": [ { "text": "1", "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ] } ], "organism part": [ { "text": "esophagus", "ontologyTerms": [ "http://purl.obolibrary.org/obo/UBERON_0001043" ], "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "sex": [ { "text": "male", "ontologyTerms": [ "http://purl.obolibrary.org/obo/PATO_0000384" ], "tag": "attribute" } ], "title": [ { "text": "T_007 rep2" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA6087989", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2019-09-07T05:34:17.766Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA6087989" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA6087989{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA6087989/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA6087989/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA6087989" } } }, { "name": "E-MTAB-8491:Kasumi7_ATACseq", "accession": "SAMEA6141225", "sraAccession": "ERS3941500", "webinSubmissionAccountId": "Webin-24", "taxId": 9606, "status": "PUBLIC", "release": "2020-10-18T17:05:30Z", "update": "2024-02-07T00:43:07.123Z", "submitted": "2019-10-31T17:04:39Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2020-10-18T17:05:30Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2019-10-31T17:04:39Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA6141225", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "Aichi Medical University" } ], "INSDC first public": [ { "text": "2020-10-18T17:05:30Z" } ], "INSDC last update": [ { "text": "2019-10-31T17:04:39Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS3941500" } ], "Submitter Id": [ { "text": "E-MTAB-8491:Kasumi7_ATACseq", "tag": "Namespace:Aichi Medical University" } ], "broker name": [ { "text": "ArrayExpress", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0009737" ] } ], "cell line": [ { "text": "Kasumi-7", "tag": "attribute" } ], "common name": [ { "text": "human", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ] } ], "description": [ { "text": "Protocols: Cells were lysed and nuclei were collected. Nuclei were incubated with Tn5 transposase in tagmentation buffer (Nextra, Illumina Inc., San Diego, CA, USA). After tagmentation, PCR amplification and library purification were performed for sequencing Nuclei were incubated with Tn5 transposase in tagmentation buffer (Nextra, Illumina Inc., San Diego, CA, USA). After tagmentation, PCR amplification and library purification were performed for sequencing" } ], "developmental stage": [ { "text": "adult", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0001272" ], "tag": "attribute" } ], "disease": [ { "text": "acute lymphoblastic leukemia", "tag": "attribute" } ], "genotype": [ { "text": "MEF2D-HNRNPUL1", "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ], "tag": "attribute" } ], "organism part": [ { "text": "blood", "ontologyTerms": [ "http://purl.obolibrary.org/obo/UBERON_0000178" ], "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "title": [ { "text": "Kasumi7_ATACseq" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA6141225", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2019-09-26T11:04:46.275Z", "_links": 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"https://www.ebi.ac.uk/ena/browser/view/SAMEA6271919", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2019-10-25T06:04:36.850Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA6271919" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA6271919{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA6271919/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA6271919/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA6271919" } } }, { "name": "E-MTAB-8576:siNT rep1", "accession": "SAMEA6377660", "sraAccession": "ERS4143751", "webinSubmissionAccountId": "Webin-24", "taxId": 9606, "status": "PUBLIC", "release": "2020-03-01T04:03:11Z", "update": "2024-02-07T01:29:45.007Z", "submitted": "2019-12-10T09:45:04Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2020-03-01T04:03:11Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2019-12-10T09:45:04Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA6377660", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "UNIVERSITY OF MANCHESTER" } ], "INSDC first public": [ { "text": "2020-03-01T04:03:11Z" } ], "INSDC last update": [ { "text": "2019-12-10T09:45:04Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS4143751" } ], "Submitter Id": [ { "text": "E-MTAB-8576:siNT rep1", "tag": "Namespace:UNIVERSITY OF MANCHESTER" } ], "broker name": [ { "text": "ArrayExpress", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0009737" ] } ], "cell line": [ { "text": "OE19", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0002308" ], "tag": "attribute" } ], "cell type": [ { "text": "epithelial cell", "ontologyTerms": [ "http://purl.obolibrary.org/obo/CL_0000066" ], "tag": "attribute" } ], "common name": [ { "text": "human", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ] } ], "description": [ { "text": "Protocols: OE19 cells were treated with either siNT or siERBB2 for 72 hours and cells were trypsinised and collected. ATAC-seq was carried out as described in Corces et al (2017) Nature (https://www.nature.com/articles/nmeth.4396) ATAC-seq library was constructed as described in Corces et al (2017) Nature (https://www.nature.com/articles/nmeth.4396)" } ], "disease": [ { "text": "esophageal carcinoma", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0002916" ], "tag": "attribute" } ], "genotype": [ { "text": "wild type genotype", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0005168" ], "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ], "tag": "attribute" } ], "organism part": [ { "text": "esophagus", "ontologyTerms": [ "http://purl.obolibrary.org/obo/UBERON_0001043" ], "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "title": [ { "text": "siNT rep1" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA6377660", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2019-11-16T03:51:18.717Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA6377660" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA6377660{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA6377660/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA6377660/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA6377660" } } }, { "name": "E-MTAB-8676:rs411 edited 3 (SPI1 -/-)", "accession": "SAMEA6479266", "sraAccession": "ERS4243749", "webinSubmissionAccountId": "Webin-24", "taxId": 9606, "status": "PUBLIC", "release": "2020-06-05T04:03:52Z", "update": "2024-02-07T01:57:50.333Z", "submitted": "2020-01-16T11:41:59Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2020-06-05T04:03:52Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2020-01-16T11:41:59Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA6479266", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "Division of Immunology and Allergy, The Children’s Hospital of Philadelphia, Abramson Research Center" } ], "INSDC first public": [ { "text": "2020-06-05T04:03:52Z" } ], "INSDC last update": [ { "text": "2020-01-16T11:41:59Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS4243749" } ], "Submitter Id": [ { "text": "E-MTAB-8676:rs411 edited 3 (SPI1 -/-)", "tag": "Namespace:Division of Immunology and Allergy, The Children’s Hospital of Philadelphia, Abramson Research Center" } ], "broker name": [ { "text": "ArrayExpress", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0009737" ] } ], "cell line": [ { "text": "RS4;11", "tag": "attribute" } ], "cell type": [ { "text": "lymphoblast", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0000572" ], "tag": "attribute" } ], "common name": [ { "text": "human", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ] } ], "description": [ { "text": "Protocols: RS4:11 cells were electroporated alone (unedited, SPI1+/+) or with CAS9 and a guide RNA sequence (GGGGGUGGAAGUCCCAGUAA) targeting exon three of SPI1 (CRISPR Knockout Pool, Synthego). Editing efficiency approached 50%. Clonal populations of mono (SPI1+/-) and biallelically edited cells (SPI1-/-) were obtained via limiting dilution and clonal expansion. Edits were confirmed via Sanger sequencing and with PU.1 immunoblots. Cell aliquots of 100,000 were washed twice and then resuspended in cold lysis buffer before being spun down. The supernatants were discarded, and then nuclei were resuspended in cold transposition reaction mix from the Illumina Tagment DNA Enzyme kit. The transposition reaction was incubated at 37°C for 45 min. Immediately following transposition, 10µl of 3M Sodium Acetate was added to the DNA which was then purified using a Qiagen MinElute Kit. Transposed DNA fragments were PCR amplified for 12 cycles using NEBNext High-Fidelity 2x PCR Master Mix(NEB) with Nextera primers (Illumina). The PCR reaction was cleaned up using AMPureXP beads (Agencourt)" } ], "developmental stage": [ { "text": "adult", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0001272" ], "tag": "attribute" } ], "disease": [ { "text": "acute lymphoblastic leukemia", "tag": "attribute" } ], "genotype": [ { "text": "SPI1 -/-", "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ], "tag": "attribute" } ], "organism part": [ { "text": "bone marrow", "ontologyTerms": [ "http://purl.obolibrary.org/obo/UBERON_0002371" ], "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "title": [ { "text": "rs411 edited 3 (SPI1 -/-)" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA6479266", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2019-12-07T04:28:37.643Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA6479266" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA6479266{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA6479266/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA6479266/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA6479266" } } }, { "name": "E-MTAB-8983:CM_ATACseq_batch1_rep2", "accession": "SAMEA6798318", "sraAccession": "ERS4525982", "webinSubmissionAccountId": "Webin-24", "taxId": 9606, "status": "PUBLIC", "release": "2020-06-08T04:05:47Z", "update": "2024-02-07T05:03:57.497Z", "submitted": "2020-04-23T10:38:07Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2020-06-08T04:05:47Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2020-04-23T10:38:07Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA6798318", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "UNIVERSITY OF CHICAGO" } ], "INSDC first public": [ { "text": "2020-06-08T04:05:47Z" } ], "INSDC last update": [ { "text": "2020-04-23T10:38:07Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS4525982" } ], "Submitter Id": [ { "text": "E-MTAB-8983:CM_ATACseq_batch1_rep2", "tag": "Namespace:UNIVERSITY OF CHICAGO" } ], "broker name": [ { "text": "ArrayExpress", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0009737" ] } ], "cell line": [ { "text": "H19101", "tag": "attribute" } ], "cell type": [ { "text": "cardiac muscle cell", "ontologyTerms": [ "http://purl.obolibrary.org/obo/CL_0000746" ], "tag": "attribute" } ], "common name": [ { "text": "human", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ] } ], "description": [ { "text": "Protocols: Cardiomyocytes were harvested by washing once with 1X PBS followed by incubation in 4 mL TrypLE (Life Technologies 12604-021) at 37°C for 5 min. After incubation, 4 mL lactate media (RPMI 1640 minus D-glucose plus L-glutamine (Life Technologies #11879020), supplemented with 0.5 mg/mL recombinant human albumin (Sigma 70024-90-7), 5 mM sodium DL-lactate (Sigma 72-17-3), 213 μg/mL L-ascorbic acid 2-phosphate (Sigma 70024-90-7) and 1X Pen/Strep) was added to the TrypLE and a 1 mL pipet was used to dislodge cells. Cells were strained once with a 100 μM strainer and then once with a 40 μM strainer. Cells were pelleted at 500xg and then resuspended in PBS and counted. 50,000 cells were used for each ATAC-seq experiment. Nucleic acid was extracted as part of the ATAC-seq protocol. Briefly, 50,000 cells were washed in cold PBS and resuspended in 50 ul cold lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Igepal CA-630) and centrifuged for 10 minutes at 4 degrees C, 500 x g. Nuclei were resuspended in the transposase reaction buffer (25 ul 2x TD reaction buffer from Nextera DNA library prep kit, 2.5 ul TDE1 Tn5 enzyme, 22.5 ul water) and incuated at 37 degrees for 30 minutes. DNA was purified from the reaction by purification on a Qiagen MinElute column according to manufacturers instructions. Purified DNA was used immediately for PCR amplification of transposed DNA using custom primers (Buenrostro et al 2013 PMID 24097267), cleaned using Ampure XP beads to enrich for fragments between 300-700 bp and analyzed on an Agilent Bioanalyzer High Sensitivity chip." } ], "disease": [ { "text": "normal", "ontologyTerms": [ "http://purl.obolibrary.org/obo/PATO_0000461" ], "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ], "tag": "attribute" } ], "progenitor cell type": [ { "text": "induced pluripotent stem cell", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0004905" ], "tag": "attribute" } ], "replicate": [ { "text": "2", "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "title": [ { "text": "CM_ATACseq_batch1_rep2" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA6798318", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2020-02-22T06:29:18.373Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA6798318" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA6798318{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA6798318/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA6798318/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA6798318" } } }, { "name": "E-MTAB-8994:CP-A", "accession": "SAMEA6801481", "sraAccession": "ERS4529140", "webinSubmissionAccountId": "Webin-24", "taxId": 9606, "status": "PUBLIC", "release": "2020-09-30T17:05:47Z", "update": "2024-02-07T05:05:06.415Z", "submitted": "2020-04-24T23:26:16Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2020-09-30T17:05:47Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2020-04-24T23:26:16Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA6801481", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "UNIVERSITY OF MANCHESTER" } ], "INSDC first public": [ { "text": "2020-09-30T17:05:47Z" } ], "INSDC last update": [ { "text": "2020-04-24T23:26:16Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS4529140" } ], "Submitter Id": [ { "text": "E-MTAB-8994:CP-A", "tag": "Namespace:UNIVERSITY OF MANCHESTER" } ], "broker name": [ { "text": "ArrayExpress", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0009737" ] } ], "cell line": [ { "text": "CP-A", "tag": "attribute" } ], "cell type": [ { "text": "epithelial cell", "ontologyTerms": [ "http://purl.obolibrary.org/obo/CL_0000066" ], "tag": "attribute" } ], "common name": [ { "text": "human", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ] } ], "description": [ { "text": "Protocols: CP-A cells were trypsinised and collected. 50,000 cells were lysed in ATAC lysis buffer and Tn5 reactions were performed as described in Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. 2013. Jason D. Buenrostro, Paul G. Giresi, Lisa C. Zaba, Howard Y. Chang and William J. Greenleaf. doi:10.1038/nmeth.2688 Libraries were constructed by amplifying transposed DNA with Illumina Nextera adapters" } ], "disease": [ { "text": "Barrett's esophagus", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0000280" ], "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ], "tag": "attribute" } ], "organism part": [ { "text": "esophagus", "ontologyTerms": [ "http://purl.obolibrary.org/obo/UBERON_0001043" ], "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "title": [ { "text": "CP-A" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA6801481", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2020-02-22T06:48:00.616Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA6801481" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA6801481{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA6801481/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA6801481/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA6801481" } } }, { "name": "E-MTAB-9087:NPC14_rep3", "accession": "SAMEA6847283", "sraAccession": "ERS4574881", "webinSubmissionAccountId": "Webin-24", "taxId": 9606, "status": "PUBLIC", "release": "2021-05-01T00:23:33Z", "update": "2024-02-07T23:22:27.452Z", "submitted": "2020-05-19T11:27:51Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2021-05-01T00:23:33Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2021-05-27T04:10:04Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA6847283", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, 19104, PA, USA Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, 19104, PA, USA Divisions of Genetics and Endocrinology, Children’s Hospital of Philadelphia, Philadelphia, 19104, PA, USA" } ], "INSDC first public": [ { "text": "2021-05-01T00:23:33Z" } ], "INSDC last update": [ { "text": "2021-05-27T04:10:04Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS4574881" } ], "Submitter Id": [ { "text": "E-MTAB-9087:NPC14_rep3", "tag": "Namespace:Center for Spatial and Functional Genomics, Children’s Hospital of Philadelphia, Philadelphia, 19104, PA, USA Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, 19104, PA, USA Divisions of Genetics and Endocrinology, Children’s Hospital of Philadelphia, Philadelphia, 19104, PA, USA" } ], "broker name": [ { "text": "ArrayExpress", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0009737" ] } ], "cell line": [ { "text": "CHOPWT14", "tag": "attribute" } ], "cell type": [ { "text": "neuronal stem cell", "ontologyTerms": [ "http://purl.obolibrary.org/obo/CL_0000047" ], "tag": "attribute" } ], "common name": [ { "text": "human", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ] } ], "description": [ { "text": "Protocols: Five replicates of CHOPWT10 and CHOPWT14 NPCs or CHOPWT10 and CHOPWT14 neurons were harvested using Accutase, followed by a DPBS wash, then counted. 50,000 cells of each sample were spun down at 550 ×g for 5 min at 4°C. The cell pellet was then resuspended in 50 μl cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and spun down immediately at 550 ×g for 10 min, 4°C. Frozen NPCs from donor CHOPWT10 and CHOPWT14 were obtained from CHOP stem cell core and thawed slowly in 37°C water bath. The thawed cells were gently washed in Neural Expansion Media (49% Neurobasal Media (ThermoFisher, cat# 21103049), 49% Advanced DMEM/F12 (ThermoFisher, cat# 12634010) and 2% 50X Neural Induction Supplement) in a 15 ml conical tube, followed by centrifuging at 300x g for 5 mins. Cells were resuspended in 1 ml pre-warmed Neural Expansion Media with Rock inhibitor (Y-27632 compound, Stem Cell Technologies, cat# 72304) at a final concentration of 10 μM and a cell count performed. NPCs were seeded at a density of 150k cells/cm2 onto hESC-qualified Matrigel-coated plates (Corning, cat# 354277) in 2.5 ml/well Neural Expansion Media and cultured at 37°C in a humidified cell culture incubator with 5% CO2. The day after, the medium was changed to remove the Y-27632 compound. NPCs were expanded for 6-7 days in 2.5 ml Neural Expansion Media exchanged every 48 hours before harvesting. The nuclei were resuspended on ice in the transposition reaction mix (2x TD Buffer, 2.5ul Tn5 Transposase and Nuclease Free H2O) (Illumina Cat #FC-121-1030, Nextera) on ice and the transposition reaction was incubated at 37°C for 45 min. The transposed DNA was then purified using a the MinElute Kit (Qiagen) adjusted to 10.5 μl elution buffer. The transposed DNA was converted into libraries using NEBNext High Fidelity 2x PCR Master Mix (NEB) and the Nextera Index Kit (illumina) by PCR amplification for 12 cycles. The PCR reaction was subsequently cleaned up using AMPureXP beads (Agencourt), checked on a Bioanalyzer 2100 (Agilent) high sensitivity DNA Chip (Aglient)" } ], "developmental stage": [ { "text": "adult", "tag": "attribute" } ], "disease": [ { "text": "normal", "ontologyTerms": [ "http://purl.obolibrary.org/obo/PATO_0000461" ], "tag": "attribute" } ], "genotype": [ { "text": "wild type genotype", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0005168" ], "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ], "tag": "attribute" } ], "organism part": [ { "text": "blood", "tag": "attribute" } ], "progenitor cell type": [ { "text": "induced pluripotent stem cell", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0004905" ], "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "title": [ { "text": "NPC14_rep3" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA6847283", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2020-02-22T10:35:03.571Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA6847283" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA6847283{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA6847283/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA6847283/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA6847283" } } }, { "name": "E-MTAB-9124:Sample 11", "accession": "SAMEA6862992", "sraAccession": "ERS4590569", "webinSubmissionAccountId": "Webin-24", "taxId": 9606, "status": "PUBLIC", "release": "2020-09-07T04:07:24Z", "update": "2024-02-07T05:36:12.179Z", "submitted": "2020-05-27T15:19:35Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2020-09-07T04:07:24Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2020-05-27T15:19:35Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA6862992", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge" } ], "INSDC first public": [ { "text": "2020-09-07T04:07:24Z" } ], "INSDC last update": [ { "text": "2020-05-27T15:19:35Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS4590569" } ], "Submitter Id": [ { "text": "E-MTAB-9124:Sample 11", "tag": "Namespace:Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge" } ], "broker name": [ { "text": "ArrayExpress", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0009737" ] } ], "cell line": [ { "text": "H9", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0003045" ], "tag": "attribute" } ], "cell type": [ { "text": "definitive endoderm cell", "tag": "attribute" } ], "common name": [ { "text": "human", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ] } ], "description": [ { "text": "Protocols: FUCCI hESCs were washed with PBS and collected by incubating with Cell Dissociation Buffer (Gibco) for 10 min at 37°C. Cells were washed with 1% PBS/BSA and incubated in 1% PBS/BSA with anti-TRA-1-60-antibody mouse monoclonal IgM (1:100, Santa Cruz Biotechnology, Inc.) for 20 min on ice, together with the secondary antibody, Alexa Fluor® 647 goat anti-mouse IgM (1:1,000, Thermo Fisher) to remove background differentiation. Cells were washed with PBS, re-suspended in 3ml of PBS and sorted into the different cell cycle phases using BD FACS AriaTM III, BD Fusion or BD Influx sorters by the Cambridge NIHR BRC Cell Phenotyping Hub. Samples were generated from two independent experiments, 100,000 cells per sample, as previously described in (Kumasaka et al., 2016) with some modifications. In brief, cells were washed with ice-cold PBS and incubated with 500μl of ice-cold sucrose buffer (10mM Tris-Cl pH 7.5, 3mM CaCl2, 2mM MgCl2 and 0.32M sucrose) for 12 min on ice. To collect the nuclei, Triton X-100 was added to a final concentration of 0.5% and cells incubated for additional 6 min on ice after mixing. Samples were then resuspended in 1ml of sucrose buffer and transferred to a fresh 1.5 ml Eppendorf tube. The nuclei were centrifuged at 1500g for 3 min at 4°C and the supernatant discarded. Nuclei pellets resuspended in 50μl of Nextera DNA Sample Preparation Kit (Illumina FC-121-1030) for tagmentation, comprising 25μl 2x Tagment DNA buffer, 20μl nuclease-free water and 5μl Tagment DNA Enzyme 1. The tagmentation reaction mixture was transferred in a 1.5ml low-binding tube and incubated at 37°C for 30 min and stopped by the addition of 250μl Buffer PB (Qiagen). The tagmented chromatin was purified using the MinElute PCR purification kit (Qiagen 28004), according to the manufacturer’s instructions, eluting in 11.5μl of buffer EB (Qiagen). For PCR amplification, 10μl of the tagmented chromatin was mixed with 2.5μl of Nextera PCR primer cocktail and 7.5μl of Nextera PCR mastermix (Illumina FC-121-1030) in low-binding PCR tube. Primers were from the Nextera Index kit (Illumina FC-121-1011), using 2.5μl of an i5 primer and 2.5μl of an i7 primer per PCR, totalling 25μl. PCR amplification was performed as follow: 72°C for 3 min and 98°C for 30 sec, followed by 12 cycles at 98°C for 10 sec 63°C for 30 sec and 72°C for 3 min. The sample volumes were then increased to 50μl by adding Qiagen EB buffer. The PCR primers were removed with 1x 0.9:1 SPRI beads (Beckman Coulter, Cat no. A63880) according to manufacturer’s instruction and samples eluted in 20μl. Following amplification, excess of primers was removed running the samples of 50ml 1% agarose TAE gel at 90V for 25 min, and size selection obtained by cutting from 120bp to 1kb. MinElute Gel Extraction kit (Qiagen 28604) was used to extract DNA, eluted in 20μl of buffer EB. Library preparation and sequencing were performed at the Wellcome Sanger Institute next-generation sequencing facility. 13 ATAC-seq libraries were prepared with one of i5 and i7 Nextera tags combination, and pooled equimolarly." } ], "developmental stage": [ { "text": "embryo", "ontologyTerms": [ "http://purl.obolibrary.org/obo/UBERON_0000922" ], "tag": "attribute" } ], "disease": [ { "text": "normal", "ontologyTerms": [ "http://purl.obolibrary.org/obo/PATO_0000461" ], "tag": "attribute" } ], "genotype": [ { "text": "wild type genotype", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0005168" ], "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ], "tag": "attribute" } ], "organism part": [ { "text": "inner cell mass", "ontologyTerms": [ "http://purl.obolibrary.org/obo/UBERON_0000087" ], "tag": "attribute" } ], "progenitor cell type": [ { "text": "embryonic stem cell", "ontologyTerms": [ "http://purl.obolibrary.org/obo/CL_0002322" ], "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "title": [ { "text": "Sample 11" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA6862992", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2020-02-22T11:33:53.607Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA6862992" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA6862992{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA6862992/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA6862992/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA6862992" } } }, { "name": "Treg_ATACseq_stim2", "accession": "SAMEA7190955", "sraAccession": "ERS4951187", "webinSubmissionAccountId": "Webin-56742", "taxId": 9606, "status": "PUBLIC", "release": "2022-05-24T08:11:07Z", "update": "2024-02-14T15:07:46.165Z", "submitted": "2020-07-02T01:51:48.459Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2022-05-24T08:11:07Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2022-05-24T08:11:07Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA7190955", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "UNIVERSITY OF ADELAIDE" } ], "INSDC first public": [ { "text": "2022-05-24T08:11:07Z" } ], "INSDC last update": [ { "text": "2022-05-24T08:11:07Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS4951187" } ], "Submitter Id": [ { "text": "Treg_ATACseq_stim2", "tag": "Namespace:UNIVERSITY OF ADELAIDE" } ], "common name": [ { "text": "human" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "title": [ { "text": "ATAC-seq data of human stimulated regulaotry T cells" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA7190955", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2020-07-02T01:51:48.459Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA7190955" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA7190955{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA7190955/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA7190955/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA7190955" } } }, { "name": "E-MTAB-9463:CLB-GA siNTC rep1", "accession": "SAMEA7197614", "sraAccession": "ERS4957837", "webinSubmissionAccountId": "Webin-24", "taxId": 9606, "status": "PUBLIC", "release": "2021-05-31T00:12:28Z", "update": "2024-02-07T23:30:42.013Z", "submitted": "2020-08-19T18:06:27Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2021-05-31T00:12:28Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2021-05-31T00:12:28Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA7197614", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "Center for Medical Genetics, Gent, Belgium Cancer Research Institute Gent, Belgium" } ], "INSDC first public": [ { "text": "2021-05-31T00:12:28Z" } ], "INSDC last update": [ { "text": "2021-05-31T00:12:28Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS4957837" } ], "Submitter Id": [ { "text": "E-MTAB-9463:CLB-GA siNTC rep1", "tag": "Namespace:Center for Medical Genetics, Gent, Belgium Cancer Research Institute Gent, Belgium" } ], "broker name": [ { "text": "ArrayExpress", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0009737" ] } ], "cell line": [ { "text": "CLB-GA", "tag": "attribute" } ], "cell type": [ { "text": "neuroblast (sensu Vertebrata)", "ontologyTerms": [ "http://purl.obolibrary.org/obo/CL_0000031" ], "tag": "attribute" } ], "common name": [ { "text": "human", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ] } ], "description": [ { "text": "Protocols: 50,000 cells were harvested and spin down for 5 min at 800g. Cells were grown in RPMI1640 medium supplemented with 10% foetal bovine serum, 2 mM L-Glutamine and 100 IU/ml penicillin/streptavidin at 37째C in a 5% CO2 humid atmosphere. For SOX11 knockdown, SMARTpool ON-TARGETplus SOX11 siRNA (cat#L-017377-01-0005) and non-targeting siRNA (cat#D-001810-01-05) were ordered from Dharmacon, each pool containing four unique siRNAs. Cells were nucleofected with 100 nM of siRNA NTC and siRNA SOX11 using the Neon Transfection System (Thermo Fisher Scientific) and subsequently seeded in T25 tissue culture plates. ATAC-seq was performed as previously described with minor changes (Buenrostro et al. 2015). 50,000 cells were lysed and fragmented using digitonin and Tn5 transposase (Nextera DNA Library Prep Kit, cat#FC-121-1030)). Samples were purified using the DNA clean & concentrator kit from Zymo (cat#D4013). The transposased DNA fragments were amplified using the KAPA HiFi HotStart Readymix (cat#07 958 927 001) and purified using Agencourt AMPure XP beads (Beckmamn Coulter, cat#A63881). Library concentrations were measured with the Illumina Kapa Library quantification kit (Lightcycler 480 qPCR mix cat#KK4854)" } ], "disease": [ { "text": "neuroblastoma", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0000621" ], "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ], "tag": "attribute" } ], "organism part": [ { "text": "bone marrow", "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "title": [ { "text": "CLB-GA siNTC rep1" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA7197614", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2020-07-02T02:27:50.744Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA7197614" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA7197614{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA7197614/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA7197614/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA7197614" } } }, { "name": "E-MTAB-9949:ATAC-seq MUTZ3", "accession": "SAMEA7745361", "sraAccession": "ERS5492710", "webinSubmissionAccountId": "Webin-24", "taxId": 9606, "status": "PUBLIC", "release": "2021-07-26T12:17:16Z", "update": "2024-02-08T11:14:10.901Z", "submitted": "2020-12-21T14:51:42Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2021-07-26T12:17:16Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2021-07-26T12:17:16Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA7745361", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "Department of Hematology, Erasmus University Medical Center" } ], "INSDC first public": [ { "text": "2021-07-26T12:17:16Z" } ], "INSDC last update": [ { "text": "2021-07-26T12:17:16Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS5492710" } ], "Submitter Id": [ { "text": "E-MTAB-9949:ATAC-seq MUTZ3", "tag": "Namespace:Department of Hematology, Erasmus University Medical Center" } ], "broker name": [ { "text": "ArrayExpress", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0009737" ] } ], "cell line": [ { "text": "MUTZ-3", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0005395" ], "tag": "attribute" } ], "cell type": [ { "text": "myeloblast", "ontologyTerms": [ "http://purl.obolibrary.org/obo/CL_0000835" ], "tag": "attribute" } ], "common name": [ { "text": "human", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ] } ], "description": [ { "text": "Protocols: 100.000 cells (MUTZ3, MOLM1) were lysed in lysis buffer The MUTZ3 cell lines were cultured in αMEM (HyClone) with 20% fetal calf serum (FCS) and 20% conditioned 5637 medium. The 293T were cultured in DMEM (Gibco) with 10% FCS. All cell lines were supplemented with 50 U/mL penicillin and 50 μg/mL streptomycin. Viable frozen AML cells were thawed and resuspended in IMDM medium supplemented with: 20% BIT medium (Stem cell technologies), 1x β-mercaptoethanol (1000x Life technologies), 6 µg/ml LDL (Sigma Aldrich), human IL6, IL3, G-CSF, GM-CSF at 20 ng/ml and FLT3, SCF at 50 ng/ml (Peprotech). Immediately after lysis, nuclei were spun at 500g for 8 minutes at 4°C. After pelleting the nuclei, we the nuclei were resuspended in Tn5 transposase reaction mix (25 ul 2X TD buffer, 2.5 ul Tn5 transposase, and 22.5 ul nucleasefree water). The transposition reaction was performed at 37°C for 30 minutes. Immediately after the transposition reaction, DNA was purified using a Qiagen MinElute kit. The transposed library was PCR amplified using Nextera primers. The PCR reaction was subsequently cleaned up using AMPureXP beads." } ], "developmental stage": [ { "text": "adult", "tag": "attribute" } ], "disease": [ { "text": "acute myeloid leukemia", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0000222" ], "tag": "attribute" } ], "genotype": [ { "text": "inv(3)", "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ], "tag": "attribute" } ], "organism part": [ { "text": "bone marrow", "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "title": [ { "text": "ATAC-seq MUTZ3" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA7745361", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2020-11-16T09:23:02.848Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA7745361" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA7745361{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA7745361/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA7745361/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA7745361" } } }, { "name": "E-MTAB-10044:SMG3", "accession": "SAMEA7872039", "sraAccession": "ERS5618493", "webinSubmissionAccountId": "Webin-24", "taxId": 9606, "status": "PUBLIC", "release": "2021-08-24T16:15:26Z", "update": "2024-02-08T16:28:51.387Z", "submitted": "2021-01-26T15:46:54Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2021-08-24T16:15:26Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2021-08-24T16:15:26Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA7872039", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "UNIVERSITY OF MANCHESTER" } ], "INSDC first public": [ { "text": "2021-08-24T16:15:26Z" } ], "INSDC last update": [ { "text": "2021-08-24T16:15:26Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS5618493" } ], "Submitter Id": [ { "text": "E-MTAB-10044:SMG3", "tag": "Namespace:UNIVERSITY OF MANCHESTER" } ], "age": [ { "text": "66", "unit": "year", "tag": "attribute" } ], "broker name": [ { "text": "ArrayExpress", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0009737" ] } ], "common name": [ { "text": "human", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ] } ], "description": [ { "text": "Protocols: NG samples 1-6 were obtained from the normal gastric cardia of surgical resections deposited in the Manchester Cancer Research Centre Biobank (REC: 07/H1003/161+5) and were accessed through an approved project (REF: 13_DAGI_05). BE5 and SMG 1-4 were obtained either by endoscopy at Cambridge University Hospitals NHS Trust (REC 15/EE/0152) or from deceased transplant organ donors (REC 15/EE/0152) at the time of organ donation. Nuclei were extracted from tissue samples as described previously (PMID: 28859074). 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Cells were collected by trypsinisation. Omni ATAC-seq protocol:Corces, M., Trevino, A., Hamilton, E. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14, 959–962 (2017). https://doi.org/10.1038/nmeth.4396 Omni ATAC-seq protocol:Corces, M., Trevino, A., Hamilton, E. et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14, 959–962 (2017). https://doi.org/10.1038/nmeth.4396" } ], "developmental stage": [ { "text": "adult", "tag": "attribute" } ], "disease": [ { "text": "esophageal adenocarcinoma", "tag": "attribute" } ], "genotype": [ { "text": "wild type genotype", "tag": "attribute" } ], "isolate": [ { "text": "not applicable", "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "tag": "attribute" } ], "organism part": [ { "text": "esophagogastric junction", "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "title": [ { "text": "Withdrawal day 3 rep2" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA8497922", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2021-03-22T04:00:26.638Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA8497922" }, "curationDomain": { "href": 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"Namespace:BioSample" } ], "INSDC center name": [ { "text": "ERASMUS MC" } ], "INSDC first public": [ { "text": "2021-04-04T04:22:42Z" } ], "INSDC last update": [ { "text": "2021-04-02T14:32:32Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS6191995" } ], "Submitter Id": [ { "text": "I20-1021-02_HUDEP2-pro-2", "tag": "Namespace:ERASMUS MC" } ], "cell line": [ { "text": "HUDEP2", "tag": "attribute" } ], "cell type": [ { "text": "Erythroid, adult", "tag": "attribute" } ], "common name": [ { "text": "human", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ] } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "title": [ { "text": "HUDEP2 proliferation ATAC-seq" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA8507187", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2021-03-22T06:49:05.619Z", 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"text": "human", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ] } ], "description": [ { "text": "Protocols: FibA, B and C were acquired from ATCC (PCS-201-010, CRL-2097, CCL-153, respectively). Fibroblasts derived from one individual with PLP1 643C>T mutation were acquired from Coriell Institute (ID:GM09546) while fibroblasts derived from three male individuals with PLP1 duplication were kindly provided by Prof. Odile Boespflug-Tanguy, LEUKOFRANCE Biobank, Biochemistry Department, Kremlin Bicetre Hospital, APHP, Paris. Fibroblasts from PMD patients were compared with sex and age matched controls as described in Table S2. For the DNA methylation assay neonatal fibroblasts were acquired from ATCC (PCS-201-010) and Coriell Institute (GM00041, GM08680), fibroblasts from middle aged donors were kindly provided by Jürgen Winkler (UKERf-4L6) and three lines were generated in UKM (UKM-F4AC). Fibroblasts from old aged donors were provided from Jürgen Winkler (UKER-fG3G, UKERf-82A, UKERf-O3H). The study was approved by the local ethical committees in Münster, Erlangen, Milan and Paris (AZ 2018-040-f-S, AZ 259_17B and Banca INSpe, CPPAU788, CNIL1406552, AFSSAPS B90298-60). Fibroblasts were cultured in fibroblast medium (FM): Dulbecco’s Modified Eagle Medium high glucose (Sigma) containing 10% FBS (Gibco), 1% nonessential amino acids (NEAA) (Sigma), 1% GlutaMAX (Gibco), and 1% penicillin/streptomycin solution (Sigma). All cell lines were negative for HIV, HCV, HBV and mycoplasma contamination. Starting with cells in lysis buffer, the amount of used DNA is regulated by the used cell number For the ATAC-seq protocol, the TD buffer and the TDE1 transposase from the Nextera Kit (Illumina) were used. The fragments size of the library was analyzed with a HighSensitivity Kit (Bioanalyzer). The rest of the protocol was performed as described in Buenrostro JD et. al. 2015 but used NEB Q5 HotStart HiFi PCR MasterMix." } ], "developmental stage": [ { "text": "fetus", "ontologyTerms": [ "http://purl.obolibrary.org/obo/UBERON_0000323" ], "tag": "attribute" } ], "disease": [ { "text": "normal", "ontologyTerms": [ "http://purl.obolibrary.org/obo/PATO_0000461" ], "tag": "attribute" } ], "experimental variable": [ { "text": "fibroblasts", "ontologyTerms": [ "http://purl.obolibrary.org/obo/CL_0000057" ], "tag": "attribute" } ], "individual": [ { "text": "CCL-153", "tag": "attribute" } ], "individual_short": [ { "text": "S153", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0005724" ], "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ], "tag": "attribute" } ], "organism part": [ { "text": "lung fibroblast", "ontologyTerms": [ "http://purl.obolibrary.org/obo/CL_0002553" ], "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "sex": [ { "text": "male", "ontologyTerms": [ "http://purl.obolibrary.org/obo/PATO_0000384" ], "tag": "attribute" } ], "title": [ { "text": "Fib C1" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA8567078", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2021-03-27T09:24:45.395Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA8567078" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA8567078{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA8567078/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA8567078/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA8567078" } } }, { "name": "E-MTAB-10444:Th1 2h L", "accession": "SAMEA8693443", "sraAccession": "ERS6377927", "webinSubmissionAccountId": "Webin-24", "taxId": 9606, "status": "PUBLIC", "release": "2021-09-09T17:08:15Z", "update": "2024-02-08T20:04:34.161Z", "submitted": "2021-05-05T16:40:23Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2021-09-09T17:08:15Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2021-09-09T17:08:15Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA8693443", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "Linkoping University" } ], "INSDC first public": [ { "text": "2021-09-09T17:08:15Z" } ], "INSDC last update": [ { "text": "2021-09-09T17:08:15Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS6377927" } ], "Submitter Id": [ { "text": "E-MTAB-10444:Th1 2h L", "tag": "Namespace:Linkoping University" } ], "broker name": [ { "text": "ArrayExpress", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0009737" ] } ], "cell type": [ { "text": "naive T cell", "ontologyTerms": [ "http://purl.obolibrary.org/obo/CL_0000084" ], "tag": "attribute" } ], "common name": [ { "text": "human", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ] } ], "description": [ { "text": "Protocols: Naïve T-cells were isolated from peripheral blood mononuclear cells (PBMCs) by magnetic bead separation using a Naive CD4+ T Cell Isolation Kit II (Miltenyi Biotec). The PBMCs were isolated from the buffy coat fraction of human blood using phase separation over lymphoprep (Axis Shields). Stimulation towards Th1 differentiation for 0.5, 1, 2, 6 and 24h. Specifically the cells were treated with a 1/1 ratio of Dynabeads® Human T-Activator CD3/CD28 (Thermofisher), recombinant IL-2 (10 ng/ml), recombinant IL-12 (5 ng/ml) and anti-IFNG (MAB285) (5 µg/ml) (Rnd Systems) in RPMI 1640 media (Gibco). For the Progesterone treated samples: Sampels were pre-incubated with 50 µM Progesterone (P4) for 12-14h prior to experiment and then reconstituted with fresh media containing above 50 µM P4 and above mentioned TH1 stimulation reagetnts to start the reaction. Non-progeterone treated sample were pre-incubated and reconstituted in growth media without P4. DNA was extracted from 50000 cells per sample in accordance with the OMNI-ATAC-seq method. Corces et al. Nature Methods 2017 Libarary construction was carried out in accordance with the OMNI-ATAC-seq method. Corces et al. Nature Methods 2017. Illumina NEXTERA primers and sequencing adapters were used to construct the index." } ], "developmental stage": [ { "text": "adult", "tag": "attribute" } ], "disease": [ { "text": "normal", "ontologyTerms": [ "http://purl.obolibrary.org/obo/PATO_0000461" ], "tag": "attribute" } ], "individual": [ { "text": "L", "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ], "tag": "attribute" } ], "organism part": [ { "text": "blood", "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "sex": [ { "text": "female", "ontologyTerms": [ "http://purl.obolibrary.org/obo/PATO_0000383" ], "tag": "attribute" } ], "stimulus": [ { "text": "Anti-CD3/CD28, IL2 and IL12", "tag": "attribute" } ], "title": [ { "text": "Th1 2h L" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA8693443", "duo": [] } 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A total of 50,000 viable cells were used to resuspend and isolate nuclei; Then, chromatin was fragmented using Tn5 transposase and amplified." } ], "disease": [ { "text": "non-small cell lung cancer", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0003060" ], "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ], "tag": "attribute" } ], "organism part": [ { "text": "lung", "ontologyTerms": [ "http://purl.obolibrary.org/obo/UBERON_0002048" ], "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "title": [ { "text": "Sample 2" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA10273846", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2021-10-06T17:28:40.854Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA10273846" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA10273846{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA10273846/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA10273846/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA10273846" } } }, { "name": "E-MTAB-11044:T21_2_1", "accession": "SAMEA10379577", "sraAccession": "ERS8033025", "webinSubmissionAccountId": "Webin-24", "taxId": 9606, "status": "PUBLIC", "release": "2022-06-15T12:17:01Z", "update": "2024-02-15T05:13:38.100Z", "submitted": "2021-10-15T12:03:20Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2022-06-15T12:17:01Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2022-06-15T12:17:01Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA10379577", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "INSERM Gustave Roussy institute" } ], "INSDC first public": [ { "text": "2022-06-15T12:17:01Z" } ], "INSDC last update": [ { "text": "2022-06-15T12:17:01Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS8033025" } ], "Submitter Id": [ { "text": "E-MTAB-11044:T21_2_1", "tag": "Namespace:INSERM Gustave Roussy institute" } ], "broker name": [ { "text": "ArrayExpress", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0009737" ] } ], "cell type": [ { "text": "CD34-negative, CD41-positive, CD42-positive megakaryocyte cell", "tag": "attribute" } ], "common name": [ { "text": "human", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ] } ], "description": [ { "text": "Protocols: The CD41+/CD42+ MK were sorted (10 000 to 30 000 cells). Cells were submitted to cell lysis, transposition, and purification steps according to Illumina protocol. The transposed DNA fragments were amplified by PCR 12 times using adapters from the Nextera Index Kit (Illumina). PCR purification was performed using MinElute PCR Purification Kit (Qiagen, 28004) to remove large fragments and remaining primers. Library quality was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies 5067-4626)." } ], "developmental stage": [ { "text": "embryo", "tag": "attribute" } ], "disease": [ { "text": "Down syndrome", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0001064" ], "tag": "attribute" } ], "genotype": [ { "text": "wild type genotype", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0005168" ], "tag": "attribute" } ], "karyotype": [ { "text": "trisomy", "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ], "tag": "attribute" } ], "organism part": [ { "text": "embryo", "tag": "attribute" } ], "progenitor cell type": [ { "text": "induced pluripotent stem cell", "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "title": [ { "text": "T21_2_1" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA10379577", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2021-10-15T11:03:41.924Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA10379577" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA10379577{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA10379577/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA10379577/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA10379577" } } }, { "name": "E-MTAB-11625:Sample 4", "accession": "SAMEA14090972", "sraAccession": "ERS11694094", "webinSubmissionAccountId": "Webin-24", "taxId": 9606, "status": "PUBLIC", "release": "2022-09-19T00:26:59Z", "update": "2024-02-20T22:29:13.306Z", "submitted": "2022-04-13T15:58:46Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2022-09-19T00:26:59Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2022-09-19T00:26:59Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA14090972", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "Institut Necker Enfants Malades (INEM), INSERM U1151/CNRS UMS 8253, Universite de Paris, Paris, France." } ], "INSDC first public": [ { "text": "2022-09-19T00:26:59Z" } ], "INSDC last update": [ { "text": "2022-09-19T00:26:59Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS11694094" } ], "Submitter Id": [ { "text": "E-MTAB-11625:Sample 4", "tag": "Namespace:Institut Necker Enfants Malades (INEM), INSERM U1151/CNRS UMS 8253, Universite de Paris, Paris, France." } ], "age": [ { "text": "91", "unit": "year", "tag": "attribute" } ], "broker name": [ { "text": "ArrayExpress" } ], "cell_type": [ { "text": "memory B cell", "tag": "attribute" } ], "common name": [ { "text": "human" } ], "description": [ { "text": "Protocols: All spleen in this study were collected from organ donors who died from stroke or head trauma. None of them had lymphoma or autoimmune disease. Immediately after splenectomy, mononuclear cells were isolated from crushed pieces of splenic tissue by ficoll density-gradient centrifugation and stored in liquid nitrogen. After thawing, mononuclear cells were counted and stained with antibodies directed against surface markers. CD21hiCD20hi (CD21high IgG+ memory B cell) and CD21intCD20int memory B cell subsets (CD21int IgG+ memory B cell) were then bulk FACS-sorted (AriaIII) from gated IgG+ switched memory B cells (IgG+CD27+CD20+IgD-) in parallel with naives B cells (CD20+CD38lowCD24intCD27-IgD+CD3-CD14-CD16+). Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) was performed on 50000 cells of each sorted population according to published methods (Buenrostro, Nature Methods, 2013, PMID: 24097267). Libraries were amplified and prepared according to published methods (Buenrostro, Nature Methods, 2013, PMID: 24097267)." } ], "developmental stage": [ { "text": "adult", "tag": "attribute" } ], "disease": [ { "text": "normal", "tag": "attribute" } ], "immunophenotype": [ { "text": "CD21high IgG+", "tag": "attribute" } ], "individual": [ { "text": "HD71", "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "tag": "attribute" } ], "organism part": [ { "text": "spleen", "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "sex": [ { "text": "female", "tag": "attribute" } ], "title": [ { "text": "Sample 4" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA14090972", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2022-04-13T14:59:17.522Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA14090972" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA14090972{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA14090972/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA14090972/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA14090972" } } }, { "name": "human_islet6", "accession": "SAMEA38959168", "sraAccession": "ERS1490060", "webinSubmissionAccountId": "Webin-43179", "taxId": 9606, "status": "PUBLIC", "release": "2017-01-13T17:01:56Z", "update": "2024-02-03T04:52:51.688Z", "submitted": "2017-01-04T12:58:18Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2017-01-13T17:01:56Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2017-01-04T12:58:18Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA38959168", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "OXFORD CENTRE FOR DIABETES, ENDOCRINOLOGY & METABOLISM" } ], "INSDC first public": [ { "text": "2017-01-13T17:01:56Z" } ], "INSDC last update": [ { "text": "2017-01-04T12:58:18Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS1490060" } ], "Submitter Id": [ { "text": "human_islet6", "tag": "Namespace:OXFORD CENTRE FOR DIABETES, ENDOCRINOLOGY & METABOLISM" } ], "common name": [ { "text": "human", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ] } ], "efo_0000246": [ { "text": "49", "tag": "attribute" } ], "efo_0004340": [ { "text": "26", "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "sex": [ { "text": "male", "ontologyTerms": [ "http://purl.obolibrary.org/obo/PATO_0000384" ], "tag": "attribute" } ], "tissue type": [ { "text": "Pancreatic islet of Langerhans", "tag": "attribute" } ], "title": [ { "text": "Human islet ATAC-seq data" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA38959168", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2018-12-07T05:58:16.641Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA38959168" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA38959168{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA38959168/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA38959168/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA38959168" } } }, { "name": "HPSI1013i-hiaf_2 derived macrophage day 34 with IFNg", "accession": "SAMEA103885388", "domain": "self.BioSamplesMigration", "taxId": 9606, "status": "PUBLIC", "release": "2016-09-27T23:00:00Z", "update": "2023-10-28T01:55:03.574Z", "submitted": "2018-06-06T13:36:36.835Z", "characteristics": { "SRA accession": [ { "text": "ERS1677776" } ], "age": [ { "text": "65-69", "unit": "year" } ], "cell type": [ { "text": "iPSC derived cell line", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0005740" ] } ], "description": [ { "text": "Macrophages derived from induced pluripotent stem cell HPSI1013i-hiaf_2 day 34 after start of differentiation, treated with interferon gamma." } ], "differentiation start date": [ { "text": "2015/06/18" } ], "disease state": [ { "text": "normal", "ontologyTerms": [ "http://purl.obolibrary.org/obo/PATO_0000461" ] } ], "ethnicity": [ { "text": "White - White British" } ], "material": [ { "text": "cell line", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0000322" ] } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ] } ], "project": [ { "text": "HipSci" } ], "sampling date": [ { "text": "2015/07/22" } ], "sex": [ { "text": "male", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0001266" ] } ], "target cell type": [ { "text": "macrophage", "ontologyTerms": [ "http://purl.obolibrary.org/obo/CL_0000235" ] } ], "time point": [ { "text": "day 34", "unit": "day" } ], "treatment": [ { "text": "interferon gamma", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0003024" ] } ] }, "relationships": [ { "source": "SAMEA103885388", "type": "derived from", "target": "SAMEA7010668" }, { "source": "SAMEG317083", "type": "has member", "target": "SAMEA103885388" } ], "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/data/view/ERS1677776", "duo": [] } ], "submittedVia": "JSON_API", "create": "2018-06-06T13:36:36.835Z", "organization": [ { "Name": "Wellcome Trust Sanger Institue", "URL": "http://www.sanger.ac.uk" } ], "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA103885388" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA103885388{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA103885388/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA103885388/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA103885388" } } }, { "name": "E-MTAB-6562:Sample 1", "accession": "SAMEA104664386", "sraAccession": "ERS2265769", "webinSubmissionAccountId": "Webin-24", "taxId": 9606, "status": "PUBLIC", "release": "2018-08-16T17:02:55Z", "update": "2024-02-04T22:34:35.762Z", "submitted": "2018-03-02T15:53:14Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2018-08-16T17:02:55Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2018-03-02T15:53:14Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA104664386", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "Center for Medical Genetics, Gent, Belgium Cancer Research Institute Gent, Belgium" } ], "INSDC first public": [ { "text": "2018-08-16T17:02:55Z" } ], "INSDC last update": [ { "text": "2018-03-02T15:53:14Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS2265769" } ], "Submitter Id": [ { "text": "E-MTAB-6562:Sample 1", "tag": "Namespace:Center for Medical Genetics, Gent, Belgium Cancer Research Institute Gent, Belgium" } ], "broker name": [ { "text": "ArrayExpress", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0009737" ] } ], "cell line": [ { "text": "IMR-32", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0001195" ], "tag": "attribute" } ], "cell type": [ { "text": "neuroblast", "ontologyTerms": [ "http://purl.obolibrary.org/obo/CL_0000337" ], "tag": "attribute" } ], "common name": [ { "text": "human", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ] } ], "description": [ { "text": "Protocols: 50,000 cells were harvested and spin down for 5 min at 800g. Cells were grown in RPMI1640 medium supplemented with 10% foetal bovine serum, 2 mM L-Glutamine and 100 IU/ml penicillin/streptavidin at 37°C in a 5% CO2 humid atmosphere ATAC-seq was performed as previously described with minor changes ( doi: 10.1002/0471142727.mb2129s109, Buenrostro et al. 2015). 50,000 cells were lysed and fragmented using digitonin and Tn5 transposase (Illumina). Samples were purified using the MinElute kit (Qiagen) The transposased DNA fragments were amplified and purified using Agencourt AMPure XP beads (Beckmamn Coulter). Library concentrations were measured with the Illumina Kapa Library quantification kit (Lightcycler 480 qPCR mix cat.no. KK4854)" } ], "disease": [ { "text": "neuroblastoma", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0000621" ], "tag": "attribute" } ], "metastatic site": [ { "text": "abdominal mass", "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ], "tag": "attribute" } ], "organism part": [ { "text": "brain", "ontologyTerms": [ "http://purl.obolibrary.org/obo/UBERON_0000955" ], "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "title": [ { "text": "Sample 1" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA104664386", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2019-03-30T03:01:33.984Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA104664386" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA104664386{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA104664386/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA104664386/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA104664386" } } }, { "name": "E-MTAB-6617:Sample 4", "accession": "SAMEA104717430", "sraAccession": "ERS2318813", "webinSubmissionAccountId": "Webin-24", "taxId": 9606, "status": "PUBLIC", "release": "2018-08-31T17:03:36Z", "update": "2024-02-06T14:35:27.987Z", "submitted": "2018-03-23T15:03:15Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2018-08-31T17:03:36Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2018-03-23T15:03:15Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA104717430", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "The Children’s Hospital of Philadelphia" } ], "INSDC first public": [ { "text": "2018-08-31T17:03:36Z" } ], "INSDC last update": [ { "text": "2018-03-23T15:03:15Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS2318813" } ], "Submitter Id": [ { "text": "E-MTAB-6617:Sample 4", "tag": "Namespace:The Children’s Hospital of Philadelphia" } ], "broker name": [ { "text": "ArrayExpress", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0009737" ] } ], "cell type": [ { "text": "CD4-positive helper T cell", "ontologyTerms": [ "http://purl.obolibrary.org/obo/CL_0000492" ], "tag": "attribute" } ], "common name": [ { "text": "human", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ] } ], "description": [ { "text": "Protocols: The following cells were sorted from human children healthy donor tonsils: naive CD4+CD45RO- T cells (Naive) and CD4+CD45RO+CD25-CXCR5hiPD1hi follicular helper CD4+ T cells (TFH). For each of the TFH and Naive libraries, 50,000 live cells were harvested. The ATAC-seq libraries were generated following a previously published protocol (Buenrostro et al., Nature Methods, 2013). The nuclei were isolated from the 50,000 cells. The isolated nuclei were treated with Tn5 Transposes from Nextera DNA Sample Preparation Kit and the transposed DNA was purified using a Qiagen MinElute Kit. The transposed DNA libraries were amplified by PCR for 12 cycles and isolated by Ampure XP beads." } ], "developmental stage": [ { "text": "juvenile stage", "tag": "attribute" } ], "disease": [ { "text": "normal", "ontologyTerms": [ "http://purl.obolibrary.org/obo/PATO_0000461" ], "tag": "attribute" } ], "individual": [ { "text": "TC58", "ontologyTerms": [ "http://www.ebi.ac.uk/efo/EFO_0002865" ], "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "ontologyTerms": [ "http://purl.obolibrary.org/obo/NCBITaxon_9606" ], "tag": "attribute" } ], "organism part": [ { "text": "tonsil", "ontologyTerms": [ "http://purl.obolibrary.org/obo/UBERON_0002372" ], "tag": "attribute" } ], "phenotype": [ { "text": "CD4+CD45RO", "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "title": [ { "text": "Sample 4" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA104717430", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2019-03-30T03:07:39.386Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA104717430" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA104717430{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA104717430/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA104717430/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA104717430" } } }, { "name": "E-MTAB-11898:G2_UT_rep1", "accession": "SAMEA110195614", "sraAccession": "ERS12293289", "webinSubmissionAccountId": "Webin-24", "taxId": 9606, "status": "PUBLIC", "release": "2022-12-31T00:58:24Z", "update": "2024-02-22T05:59:31.602Z", "submitted": "2022-06-29T11:32:41Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2022-12-31T00:58:24Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2022-12-31T00:58:24Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA110195614", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "UGent" } ], "INSDC first public": [ { "text": "2022-12-31T00:58:24Z" } ], "INSDC last update": [ { "text": "2022-12-31T00:58:24Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS12293289" } ], "Submitter Id": [ { "text": "E-MTAB-11898:G2_UT_rep1", "tag": "Namespace:UGent" } ], "broker name": [ { "text": "ArrayExpress" } ], "cell line": [ { "text": "SHEP", "tag": "attribute" } ], "cell type": [ { "text": "neuroblast (sensu Vertebrata)", "tag": "attribute" } ], "common name": [ { "text": "human" } ], "description": [ { "text": "Protocols: 50,000 cells were harvested and spin down for 5 min at 800g. Cells were grown in RPMI1640 medium supplemented with 10% foetal bovine serum, 2 mM L-Glutamine and 100 IU/ml penicillin/streptavidin at 37°C in a 5% CO2 humid atmosphere, supplemented with 10% tetracyclin-free FBS to avoid leakage. For SOX11 inducible overexpression, the OriGene vector SC303275 containing the cDNA of SOX11 was amplified by PCR and the obtained fragment was gel purified and ligated into the opened NdeI site of response vector pLVX-TRE2G-Zsgreen1 (Takara, cat#631353) producing pLVX-TRE3G-Zsgreen1-IRES-hSOX11. The constructed plasmid was verified by restriction digest and sequenced by Sanger DNA sequencing (GATC). Lenti-X 293T Cells (Takara, cat#632180) were transfected with the regulator vector pLVX-pEF1a-Tet3G (cat#631353 and Lenti-X Packaging Single Shots (VSV-G) (cat#631275) according to the manufacturer’s instructions. The supernatant containing the lenti-virus was collected, filtered through a 0.45 µm filter and concentrated using PEG-IT. SH-EP cells were infected with the concentrated virus and 48 hours of incubation thereafter, the transduced cells were selected using 500 µg/ml G418. Individual clones were obtained by limiting dilution. After clonal expansion, the TET protein expression in each clone was checked by immunoblotting using TetR monoclonal antibody (Clone 9G9) (Clontech, cat#631131). In addition, induction of each expressing clone was tested after transduction with the pLVX-TRE3G-Luc control vector. Selected clones were transduced with lentivirus produced as described above from vector pLVX-TRE3G-Zsgreen1-IRES-hSOX11 and subsequently selected with 1 µg/ml puromycin. Each clone was treated with 1 ug/ml Doxycycline for induction of SOX11 expression or left unaffected in case of the control. ATAC-seq was performed as previously described with minor changes (Buenrostro et al. 2015). 50,000 cells were lysed and fragmented using digitonin and Tn5 transposase (Nextera DNA Library Prep Kit, cat#FC-121-1030)). Samples were purified using the DNA clean & concentrator kit from Zymo (cat#D4013). The transposased DNA fragments were amplified using the KAPA HiFi HotStart Readymix (cat#07 958 927 001) and purified using Agencourt AMPure XP beads (Beckmamn Coulter, cat#A63881). Library concentrations were measured with the Illumina Kapa Library quantification kit (Lightcycler 480 qPCR mix cat#KK4854)" } ], "disease": [ { "text": "neuroblastoma", "tag": "attribute" } ], "genotype": [ { "text": "doxycycline-inducible SOX11 expression clone G2", "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "tag": "attribute" } ], "organism part": [ { "text": "bone marrow", "tag": "attribute" } ], "phenotype": [ { "text": "wild type", "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "title": [ { "text": "G2_UT_rep1" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA110195614", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2022-06-29T10:32:41.616Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA110195614" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA110195614{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA110195614/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA110195614/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA110195614" } } }, { "name": "E-MTAB-12025:VCaP_Ctrl_4.fastq.gz", "accession": "SAMEA110471382", "sraAccession": "ERS12569405", "webinSubmissionAccountId": "Webin-24", "taxId": 9606, "status": "PUBLIC", "release": "2023-07-15T00:19:51Z", "update": "2024-02-27T11:13:08.002Z", "submitted": "2022-08-08T10:48:39Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2023-07-15T00:19:51Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2023-07-15T00:19:51Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA110471382", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "Institute of Oncology research (IOR)" } ], "INSDC first public": [ { "text": "2023-07-15T00:19:51Z" } ], "INSDC last update": [ { "text": "2023-07-15T00:19:51Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS12569405" } ], "Submitter Id": [ { "text": "E-MTAB-12025:VCaP_Ctrl_4.fastq.gz", "tag": "Namespace:Institute of Oncology research (IOR)" } ], "broker name": [ { "text": "ArrayExpress" } ], "cell_line": [ { "text": "VCaP", "tag": "attribute" } ], "cell_type": [ { "text": "epithelial cell", "tag": "attribute" } ], "common name": [ { "text": "human" } ], "description": [ { "text": "Protocols: Collection of 50000 cells per replicate and resuspension of the pellet in TRIzol buffer - Resuspension of nuclei in the transposition reaction mix- Incubation of the transposition reaction- Purification using Qiagen MinElute PCR Purification Kit- Elution of transposed DNA in Elution BufferRefer to DOI: 10.1002/0471142727.mb2129s109 - Amplification of DNA fragments - Purification of amplified library using Qiagen MinElute PCR Purification Kit" } ], "disease": [ { "text": "prostate cancer", "tag": "attribute" } ], "isolate": [ { "text": "not applicable", "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "tag": "attribute" } ], "organism part": [ { "text": "prostate gland", "tag": "attribute" } ], "replicate": [ { "text": "4", "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "title": [ { "text": "VCaP_Ctrl_4.fastq.gz" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA110471382", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2022-08-08T09:48:39.546Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA110471382" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA110471382{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA110471382/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA110471382/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA110471382" } } }, { "name": "E-MTAB-12076:HEK_CHIR_3d_C", "accession": "SAMEA110590496", "sraAccession": "ERS12688271", "webinSubmissionAccountId": "Webin-24", "taxId": 9606, "status": "PUBLIC", "release": "2022-09-30T00:20:53Z", "update": "2024-02-21T01:22:21.237Z", "submitted": "2022-08-10T10:57:11Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2022-09-30T00:20:53Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2022-09-30T00:20:53Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA110590496", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "Wallenberg Center for Molecular Medicine (WCMM) Department of Biomedical and Clinical Sciences (BKV) Division of Molecular Medicine and Virology (MMV) Faculty of Medicine and Health Sciences, Linkoping University, Linkoping, Sweden" } ], "INSDC first public": [ { "text": "2022-09-30T00:20:53Z" } ], "INSDC last update": [ { "text": "2022-09-30T00:20:53Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS12688271" } ], "Submitter Id": [ { "text": "E-MTAB-12076:HEK_CHIR_3d_C", "tag": "Namespace:Wallenberg Center for Molecular Medicine (WCMM) Department of Biomedical and Clinical Sciences (BKV) Division of Molecular Medicine and Virology (MMV) Faculty of Medicine and Health Sciences, Linkoping University, Linkoping, Sweden" } ], "broker name": [ { "text": "ArrayExpress" } ], "cell_line": [ { "text": "HEK293T", "tag": "attribute" } ], "cell_type": [ { "text": "embryonic kidney cell", "tag": "attribute" } ], "common name": [ { "text": "human" } ], "description": [ { "text": "Protocols: Cells collected from cell cultures, see growth protocol. HEK293T cells (HEK293Ts) were cultured in medium consisting of DMEM, high glucose (41966-029, Gibco - Thermo Fisher Scientific) supplemented with 10% Calf Bovine Serum (12133C, Sigma-Aldrich) and 10 U/ml Penicillin-Streptomycin (15276355, Gibco - Thermo Fisher Scientific). HEK293Ts were passaged by incubation in Trypsin EDTA 0.25% (25-200-056, Thermo Fisher Scientific). hESCs were cultured in Essential 8TM medium (A1517001, ThermoFisher Scientific) in plates and flasks coated with 10 mg/ml Vitronectin (A14700, ThermoFisher Scientific). Cells were passaged by incubation in 0.5 mM EDTA-PBS (stock: 0.5 M EDTA, AM9260G, Thermo Fisher Scientific). Both cell types were treated with 10 mM CHIR99021 for 4 hours, 24 hours and 3 days (n = 3 samples for each condition). Cells were collected, lysed in ice cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630), and pelleted. Pelleted nuclei were incubated in 50 ml transposition reaction mix (20034210, Illumina) at 370C for 30 minutes. Transposed DNA fragments were amplified for 13 cycles in the presence of Custom Nextera PCR primers (Buenrostro et al., 2013) using the NEBNext High-Fidelity 2x PCR Master Mix (Cat. #M0541, New England Biolabs). Libraries were purified using the High Pure PCR Production Purification Kit (11732676001, Roche / Sigma-Aldrich). Libraries were validated on an Agilent 2100 and quantified using quantitative PCR (Q-PCR)." } ], "developmental stage": [ { "text": "embryo stage", "tag": "attribute" } ], "disease": [ { "text": "normal", "tag": "attribute" } ], "genotype": [ { "text": "wild type genotype", "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "tag": "attribute" } ], "organism part": [ { "text": "kidney", "tag": "attribute" } ], "replicate": [ { "text": "3", "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "title": [ { "text": "HEK_CHIR_3d_C" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA110590496", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2022-08-10T09:57:11.116Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA110590496" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA110590496{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA110590496/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA110590496/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA110590496" } } }, { "name": "E-MTAB-12294:ATACseq U2OS", "accession": "SAMEA111468771", "sraAccession": "ERS13562801", "webinSubmissionAccountId": "Webin-24", "taxId": 9606, "status": "PUBLIC", "release": "2023-06-01T00:15:25Z", "update": "2024-02-25T21:48:27.206Z", "submitted": "2022-10-14T10:21:34Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2023-06-01T00:15:25Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2023-06-01T00:15:25Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA111468771", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "Faculty of Biology, Medicine and Health, University of Manchester" } ], "INSDC first public": [ { "text": "2023-06-01T00:15:25Z" } ], "INSDC last update": [ { "text": "2023-06-01T00:15:25Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS13562801" } ], "Submitter Id": [ { "text": "E-MTAB-12294:ATACseq U2OS", "tag": "Namespace:Faculty of Biology, Medicine and Health, University of Manchester" } ], "broker name": [ { "text": "ArrayExpress" } ], "cell_line": [ { "text": "U2OS", "tag": "attribute" } ], "common name": [ { "text": "human" } ], "description": [ { "text": "Protocols: Cells were lysed 48 h after transfection in cold lysis buffer (10mM Tris-HCL, pH 7.4, 10mMNaCl, 3mM MgCl2 and 0.1% Igepal). DNA was purified using Qiagen mini elute kit and using Ampure XP beads following the manufacturer’s instructions. Nuclei was concentrated by centrifugation at 500 g for 10 minutes at 4°C. The nuclei pellet was resuspended in nuclease free water, diluted 1:10 and quantified. The equivalent volume for 50,000 nuclei was made up to 22.5 ul with nuclease free water. Nuclei were incubated for 30 minutes at 37°C, 300 rpm, with 25 ul of 2x TD buffer and 2.5 ul tagmentation ezyme (Illumina transposase FC-121-1030). Library fragments were amplified using standard PCR and Nextera primers (Illumina) by adding 25 ul of 2x NEBnext master mix, 2.5 ul forward primer, 2.5 ul reverse primer and 20 ul transposased DNA. PCR was run for 5 cycles, 72°C, 5 minutes; 98°C 30 seconds; cycle of 98°C 10 seconds, 63°C 30 seconds, 72°C 1 minute, paused at 4°C. To determine the total number of cycles needed for the amplified library, 5 ul of the PCR mix were taken and added to a new mix containing 5 ul 2X master mix, 1 ul of each primer, 0.6 ul of 10X SYBR green and 2.4 ul H2O. In a qPCR machine, 20 cycles were run, the total number of cycles for the ATAC library was chosen according to qPCR cycle that gave 1/3 of saturation." } ], "developmental stage": [ { "text": "juvenile stage", "tag": "attribute" } ], "disease": [ { "text": "osteosarcoma", "tag": "attribute" } ], "genotype": [ { "text": "wild type genotype", "tag": "attribute" } ], "isolate": [ { "text": "not applicable", "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "tag": "attribute" } ], "organism part": [ { "text": "tibia", "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "title": [ { "text": "ATACseq U2OS" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA111468771", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2022-10-14T09:21:34.116Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA111468771" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA111468771{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA111468771/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA111468771/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA111468771" } } }, { "name": "E-MTAB-12661:D22_RoDe_REP3_RUN5", "accession": "SAMEA112655738", "sraAccession": "ERS14653290", "webinSubmissionAccountId": "Webin-24", "taxId": 9606, "status": "PUBLIC", "release": "2023-06-15T00:18:06Z", "update": "2024-02-26T00:28:57.224Z", "submitted": "2023-02-17T12:15:32.019Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2023-06-15T00:18:06Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2023-06-15T00:18:06Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA112655738", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "Istituto di Ricerche Farmacologiche \\\"Mario Negri\\\" IRCCS" } ], "INSDC first public": [ { "text": "2023-06-15T00:18:06Z" } ], "INSDC last update": [ { "text": "2023-06-15T00:18:06Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS14653290" } ], "Submitter Id": [ { "text": "E-MTAB-12661:D22_RoDe_REP3_RUN5", "tag": "Namespace:Istituto di Ricerche Farmacologiche \\\"Mario Negri\\\" IRCCS" } ], "broker name": [ { "text": "ArrayExpress" } ], "cell_type": [ { "text": "induced pluripotent stem cell", "tag": "attribute" } ], "common name": [ { "text": "human" } ], "description": [ { "text": "Protocols: Collection of 50000 cells per replicate and resuspension of the pellet in TRIzol buffer - Resuspension of nuclei in the transposition reaction mix- Incubation of the transposition reaction- Purification using Qiagen MinElute PCR Purification Kit- Elution of transposed DNA in Elution BufferRefer to DOI: 10.1002/0471142727.mb2129s109 - Amplification of DNA fragments- Purification of amplified library using Qiagen MinElute PCR Purification Kit" } ], "disease": [ { "text": "normal", "tag": "attribute" } ], "genotype": [ { "text": "wild type genotype", "tag": "attribute" } ], "isolate": [ { "text": "not applicable", "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "tag": "attribute" } ], "organism part": [ { "text": "blood", "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "sex": [ { "text": "female", "tag": "attribute" } ], "title": [ { "text": "D22_RoDe_REP3_RUN5" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA112655738", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2023-02-17T12:15:31.566Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA112655738" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA112655738{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA112655738/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA112655738/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA112655738" } } }, { "name": "E-MTAB-12684:D9_Patient_REP1_RUN2", "accession": "SAMEA112656959", "sraAccession": "ERS14654508", "webinSubmissionAccountId": "Webin-24", "taxId": 9606, "status": "PUBLIC", "release": "2023-06-23T00:21:34Z", "update": "2024-02-26T15:30:04.346Z", "submitted": "2023-02-17T15:07:57.428Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2023-06-23T00:21:34Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2023-06-23T00:21:34Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA112656959", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "Istituto di Ricerche Farmacologiche \\\"Mario Negri\\\" IRCCS" } ], "INSDC first public": [ { "text": "2023-06-23T00:21:34Z" } ], "INSDC last update": [ { "text": "2023-06-23T00:21:34Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS14654508" } ], "Submitter Id": [ { "text": "E-MTAB-12684:D9_Patient_REP1_RUN2", "tag": "Namespace:Istituto di Ricerche Farmacologiche \\\"Mario Negri\\\" IRCCS" } ], "broker name": [ { "text": "ArrayExpress" } ], "cell_type": [ { "text": "hepatocyte", "tag": "attribute" } ], "common name": [ { "text": "human" } ], "description": [ { "text": "Protocols: Day 9 of hepatocyte differentiation. Collection of 50000 cells per replicate and resuspension of the pellet in TRIzol buffer - Resuspension of nuclei in the transposition reaction mix- Incubation of the transposition reaction- Purification using Qiagen MinElute PCR Purification Kit- Elution of transposed DNA in Elution BufferRefer to DOI: 10.1002/0471142727.mb2129s109 - Amplification of DNA fragments- Purification of amplified library using Qiagen MinElute PCR Purification Kit" } ], "disease": [ { "text": "Cornelia de Lange syndrome", "tag": "attribute" } ], "genotype": [ { "text": "heterozygous missense point-mutation of NIPBL", "tag": "attribute" } ], "isolate": [ { "text": "not applicable", "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "tag": "attribute" } ], "organism part": [ { "text": "blood", "tag": "attribute" } ], "progenitor cell type": [ { "text": "induced pluripotent stem cell", "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "sex": [ { "text": "female", "tag": "attribute" } ], "title": [ { "text": "D9_Patient_REP1_RUN2" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA112656959", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2023-02-17T15:07:57.277Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA112656959" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA112656959{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA112656959/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA112656959/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA112656959" } } }, { "name": "E-MTAB-12830:ATACSeq_DEHP_1", "accession": "SAMEA112849057", "sraAccession": "ERS14855678", "webinSubmissionAccountId": "Webin-24", "taxId": 9606, "status": "PUBLIC", "release": "2023-09-03T00:29:42Z", "update": "2024-02-28T01:36:14.526Z", "submitted": "2023-03-29T12:24:10.939Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2023-09-03T00:29:42Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2023-09-03T00:29:42Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA112849057", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "Maastricht University, Maastricht, The Netherlands" } ], "INSDC first public": [ { "text": "2023-09-03T00:29:42Z" } ], "INSDC last update": [ { "text": "2023-09-03T00:29:42Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS14855678" } ], "Submitter Id": [ { "text": "E-MTAB-12830:ATACSeq_DEHP_1", "tag": "Namespace:Maastricht University, Maastricht, The Netherlands" } ], "age": [ { "text": "35", "unit": "year", "tag": "attribute" } ], "broker name": [ { "text": "ArrayExpress" } ], "cell_line": [ { "text": "Nthy-ori 3-1", "tag": "attribute" } ], "cell_type": [ { "text": "thyroid follicular cell", "tag": "attribute" } ], "common name": [ { "text": "human" } ], "description": [ { "text": "Protocols: The human epithelial thyroid cell line Nthy-ori 3-1 was plated at a density of 10,000 cells/cm2 on 6-well plates and cultured in RPMI 1640 Medium with GlutaMAX™ Supplement (61870036, Gibco), 10% FBS and Penicillin-Streptomycin (15140122, Gibco) and incubated at 37 ºC, 5% pCO2 and >95% humidity. Cells were left one day to adhere, and the following day the media was changed to culture media with DEHP (n=6) or DINP (n=6) at 1 uM in 0.5% DMSO. As solvent control, the culture media was additioned with just 0.5% DMSO (n=6). Cells were incubated for 5 days refreshing the media with the compound or DMSO only at day 3. At the end of the incubation period, cells were collected and counted manually. 50,000 cells per sample were used to prepare ATAC-Seq libraries. Libraries were prepared following the Omni-Atac protocol of Corces et al. 2017 [45] with the replacement of NP40 from the original protocol with IGEPAL (Merck, I8896-50ml). The tagmentase kit used was Illumina Tagment DNA Enzyme and Buffer Small Kit (Illumina, 20034197) and the indexes IDT® for Illumina® DNA/RNA UD Indexes Set A, Tagmentation (96 Indexes, 96 samples) (Illumina, 20027213). Seven PCR cycles were used for all samples. ATAC-Seq libraries were quantified on a Qubit 2.0 Fluorometer (ThermoFisher) and quality control checked on the 2200 TapeStation System (Agilent) or BioAnalyzer 2100 expert (Agilent)." } ], "developmental stage": [ { "text": "adult", "tag": "attribute" } ], "disease": [ { "text": "normal", "tag": "attribute" } ], "genotype": [ { "text": "wild type genotype", "tag": "attribute" } ], "growth condition": [ { "text": "human thyroid cell culture", "tag": "attribute" } ], "isolate": [ { "text": "not applicable", "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "tag": "attribute" } ], "organism part": [ { "text": "thyroid gland", "tag": "attribute" } ], "progenitor cell type": [ { "text": "", "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "sex": [ { "text": "female", "tag": "attribute" } ], "title": [ { "text": "ATACSeq_DEHP_1" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA112849057", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2023-03-29T12:24:08.423Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA112849057" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA112849057{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA112849057/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA112849057/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA112849057" } } }, { "name": "E-MTAB-13240:iPSC_G12_Patient_REP2_RUN2", "accession": "SAMEA114249662", "sraAccession": "ERS16236923", "webinSubmissionAccountId": "Webin-24", "taxId": 9606, "status": "PUBLIC", "release": "2023-11-01T00:24:37Z", "update": "2024-02-28T16:13:57.088Z", "submitted": "2023-08-10T13:36:15.816Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2023-11-01T00:24:37Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2023-11-01T00:24:37Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA114249662", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "Istituto di Ricerche Farmacologiche \\\"Mario Negri\\\" IRCCS" } ], "INSDC first public": [ { "text": "2023-11-01T00:24:37Z" } ], "INSDC last update": [ { "text": "2023-11-01T00:24:37Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS16236923" } ], "Submitter Id": [ { "text": "E-MTAB-13240:iPSC_G12_Patient_REP2_RUN2", "tag": "Namespace:Istituto di Ricerche Farmacologiche \\\"Mario Negri\\\" IRCCS" } ], "broker name": [ { "text": "ArrayExpress" } ], "cell_type": [ { "text": "induced pluripotent stem cell", "tag": "attribute" } ], "collection date": [ { "text": "not collected", "tag": "attribute" } ], "common name": [ { "text": "human" } ], "description": [ { "text": "Protocols: Collection of 50000 cells per replicate and resuspension of the pellet in TRIzol buffer - Resuspension of nuclei in the transposition reaction mix- Incubation of the transposition reaction- Purification using Qiagen MinElute PCR Purification Kit- Elution of transposed DNA in Elution BufferRefer to DOI: 10.1002/0471142727.mb2129s109 - Amplification of DNA fragments- Purification of amplified library using Qiagen MinElute PCR Purification Kit" } ], "disease": [ { "text": "Cornelia de Lange syndrome", "tag": "attribute" } ], "genotype": [ { "text": "corrected heterozygous missense point-mutation of the NIPBL gene", "tag": "attribute" } ], "geographic location (country and/or sea)": [ { "text": "not collected", "tag": "attribute" } ], "isolate": [ { "text": "not applicable", "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "tag": "attribute" } ], "organism part": [ { "text": "blood", "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "sex": [ { "text": "female", "tag": "attribute" } ], "title": [ { "text": "iPSC_G12_Patient_REP2_RUN2" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA114249662", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2023-08-10T13:36:15.556Z", "_links": { "self": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA114249662" }, "curationDomain": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA114249662{?curationdomain}", "templated": true }, "curationLinks": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA114249662/curationlinks" }, "curationLink": { "href": "https://www.ebi.ac.uk/biosamples/samples/SAMEA114249662/curationlinks/{hash}", "templated": true }, "structuredData": { "href": "https://www.ebi.ac.uk/biosamples/structureddata/SAMEA114249662" } } }, { "name": "E-MTAB-13373:Human NPCs 1", "accession": "SAMEA114458349", "sraAccession": "ERS16444993", "webinSubmissionAccountId": "Webin-24", "taxId": 9606, "status": "PUBLIC", "release": "2023-10-25T00:19:01Z", "update": "2024-02-28T14:31:28.317Z", "submitted": "2023-09-29T11:51:44.705Z", "characteristics": { "ENA-CHECKLIST": [ { "text": "ERC000011", "tag": "attribute" } ], "ENA-FIRST-PUBLIC": [ { "text": "2023-10-25T00:19:01Z", "tag": "attribute" } ], "ENA-LAST-UPDATE": [ { "text": "2023-10-25T00:19:01Z", "tag": "attribute" } ], "External Id": [ { "text": "SAMEA114458349", "tag": "Namespace:BioSample" } ], "INSDC center name": [ { "text": "Ludwig-Maximilians-Universität, Munich Faculty of Biology Anthropology and Human Genomics" } ], "INSDC first public": [ { "text": "2023-10-25T00:19:01Z" } ], "INSDC last update": [ { "text": "2023-10-25T00:19:01Z" } ], "INSDC status": [ { "text": "public" } ], "SRA accession": [ { "text": "ERS16444993" } ], "Submitter Id": [ { "text": "E-MTAB-13373:Human NPCs 1", "tag": "Namespace:Ludwig-Maximilians-Universität, Munich Faculty of Biology Anthropology and Human Genomics" } ], "broker name": [ { "text": "ArrayExpress" } ], "cell_line": [ { "text": "29B5", "tag": "attribute" } ], "cell_type": [ { "text": "neural progenitor cell", "tag": "attribute" } ], "collection date": [ { "text": "not collected", "tag": "attribute" } ], "common name": [ { "text": "human" } ], "description": [ { "text": "Protocols: Previously generated urinary stem cell derived iPS-cells (Homo sapiens) of 2 human individuals and fibroblast derived cynomolgus macaque iPSCs (Macaca fascicularis) of 2 individuals (Geuder et al. 2021) were differentiated to neural progenitor cells via dual-SMAD inhibition as three-dimensional aggregation culture (Chambers et al. 2009, Ohnuki et al. 2014). Briefly, iPSCs were dissociated and 9000 iPSCs were seeded in a low attachment U-bottom 96-well-plate in 8GMK medium consisting of GMEM (Thermo Fisher), 8% KSR (Thermo Fisher), 5.5 ml 100× NEAA (Thermo Fisher), 100 mM Sodium Pyruvate (Thermo Fisher), 50 mM 2-Mercaptoethanol (Thermo Fisher) supplemented with 500 nM A-83–01 (Sigma Aldrich), 100 nM LDN 193189 (Sigma Aldrich) and 30 µM Y27632 (biozol). Culture medium of the spheres was changed every second day until they were harvested or plated for further culture. In order to obtain stable NPC lines, spheres were dissociated on day 7 of the differentiation process using Accumax (Sigma Aldrich) and plated onto Geltrex (Thermo Fisher) coated dishes. NPCs were subsequently cultured in NPC proliferation medium (DMEM F12 (Fisher Scientific) supplemented with 2 mM GlutaMAX-I (Fisher Scientific), 20 ng/mL bFGF (Peprotech), 20 ng/mL hEGF (Miltenyi Biotec), 2% B-27 supplement (50×) minus vitamin A (Gibco), 1% N2 supplement 100× (Gibco), 200 µM L-ascorbic acid 2-phosphate (Sigma), and 100U/ml 100µg/ml penicillin-streptomycin). All cell lines have been authenticated using RNA sequencing (RNA-seq) (Geuder et al. 2021), and the current study. iPSCs of 2 clones from 2 human individuals and 2 clones of 2 cynomolgus macaque individuals were differentiated using the protocol as described above. The NPC lines were cultured in NPC proliferation medium and passaged 2 - 4 times until they were dissociated and subjected to ATAC-seq together with the respective iPSC clones. After cells were counted, 100,000 cells were pelleted at 500 rcf for 5 min, washed with 1 ml PBS and pelleted at 500 rcf for 5 min at 4 °C. The supernatant was removed completely and cells were resuspended in 100 µl chilled nuclei lysis buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2 in water, supplemented with 0.1% Tween-20, 0.1% NP40, 0.01% Digitonin and 1% BSA) by pipetting up and down three times, followed by incubation on ice for 3 min. After lysis, 1 ml of lysis wash buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2 in water, supplemented with 0.1% Tween-20 and 1% BSA) was added, and tubes were inverted three times. After counting, 50,000 nuclei were pelleted at 500 rcf for 10 min at 4°C, the supernatant was removed and nuclei were resuspended in 50 µl transposition mix (25 µl 2x TD buffer, 2.5 µl TDE1, 16.5 µl PBS, 0.5 µl 1% digitonin, 0.5 µl 10% Tween-20 and 5 µl ddH2O) by pipetting six times. Transposition reactions were incubated at 37 °C for 1 h at 1000 rpm shaking, followed by a clean-up using the DNA Clean & Concentrator-5 kit (Zymo). For library generation, 20 µl of the transposed sample was mixed with 2.5 µl 25µl p5 custom primer, 2.5 µl 25µl p7 custom primer from Buenrostro et al. 2013 and 25 µl NEBNext Ultra II Q5 2x Master Mix (NEB) and a PCR with 10 cycles was conducted as stated in the Omni-ATAC protocol. Libraries were purified using the DNA Clean & Concentrator-5 kit, run on a 2% E-Gel (Thermo Fisher) and gel excision of DNA between 150 bp and 1,500 bp was performed using the Monarch DNA Gel Excision Kit (NEB)." } ], "genotype": [ { "text": "wild type genotype", "tag": "attribute" } ], "geographic location (country and/or sea)": [ { "text": "not collected", "tag": "attribute" } ], "isolate": [ { "text": "not applicable", "tag": "attribute" } ], "organism": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] }, { "text": "Homo sapiens", "tag": "attribute" } ], "progenitor cell type": [ { "text": "induced pluripotent stem cell", "tag": "attribute" } ], "scientific_name": [ { "text": "Homo sapiens", "ontologyTerms": [ "" ] } ], "title": [ { "text": "Human NPCs 1" } ] }, "externalReferences": [ { "url": "https://www.ebi.ac.uk/ena/browser/view/SAMEA114458349", "duo": [] } ], "submittedVia": "PIPELINE_IMPORT", "create": "2023-09-29T11:51:44.408Z", "_links": { "self": { "href": 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