Published February 23, 2021
| Version 1.0.1
Journal article
Open
Enhancer hijacking activates oncogenic transcription factor NR4A3 in Acinic Cell Carcinomas of the salivary glands (datasets)
Creators
- Florian Haller1
-
Matthias Bieg2
- Rainer Will3
- Cindy Körner4
- Dieter Weichenhan5
- Alexander Bott4
-
Naveed Ishaque2
- Pavlo Lutsik5
- Evgeny A. Moskalev1
- Sarina K. Mueller6
- Marion Bähr5
- Angelika Woerner4
- Birgit Kaiser3
- Claudia Scherl6
- Marlen Haderlein7
-
Kortine Kleinheinz8
- Rainer Fietkau7
- Heinrich Iro6
-
Roland Eils2
- Arndt Hartmann1
- Christoph Plass5
- Stefan Wiemann3
- Abbas Agaimy1
- 1. Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Krankenhausstr. 8-10, 91054 Erlangen, Germany
- 2. Center for Digital Health, Berlin Institute of Health and Charité – Universitätsmedizin Berlin, Kapelle-Ufer 2, 10117 Berlin, Germany
- 3. Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
- 4. Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
- 5. Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- 6. Department of Otorhinolaryngology, Head & Neck Surgery, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Waldstrasse 1, 91054 Erlangen, Germany
- 7. Department of Radiation Therapy, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Universitätsstrasse 27, 91054 Erlangen, Germany
- 8. Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
Description
This dataset consists of processed data from CHIP-Seq experiments (peaks as bed files, and signals as bigWig files), as well as whole genome bisulfite experiments (methlyation calls as bedGraph files). Here, we profiled histone modifications (H3K27ac, H3K27me3, and H3K4me3), as well as two transcription factors (CTCF, and NR4A3), from 3 acinar cell carcinoma, as well as one normal parotid gland sample. Furthermore, we profiled DNA methylation for three acinar cell carcinoma, as well as three normal parotid gland samples. In addition you find RNA-Seq count-, and fpkm tables for 13 human samples (10 tumor samples, 3 normal samples), as well as RNA-Seq count-, and fpkm tables for 6 mouse samples (3 NR4A3 ORF transfected mouse cell lines, as well as 3 control mouse cell lines with transfected redFF construct). The following files make up the dataset:
ChIP-Seq peak files (bed format)
- AciCC1_CTCF_peaks_2167aeb49f637ea6a124e3679ce1722d.bed
- AciCC1_H3K27Ac_peaks_8e63eed24d0cc6cb362aa8c8da6f74ed.bed
- AciCC1_H3K27me3_peaks_7ba6a30bdabbf46f6e67deab447f5f98.bed
- AciCC1_H3K4me3_peaks_88cdce01aeededcdae869c5a68657d89.bed
- AciCC1_NR4A3_peaks_02be26bf1e905bcbdbb222cba4c13133.bed
- AciCC1_super_enhancer_peaks_3c3622d06160797a049f1e5b35efb068.bed
- AciCC2_CTCF_peaks_3b0fde69ad4c01f71d4a5ef07f1a8daf.bed
- AciCC2_H3K27Ac_peaks_36d1d3116fa41220ea57494961972245.bed
- AciCC2_H3K27me3_peaks_7f8f1745a20638c9db7f24c101556d12.bed
- AciCC2_H3K4me3_peaks_838e68c7c58e69ff02c6a9cea9bdfda9.bed
- AciCC2_NR4A3_peaks_9a5244e979b51e870b16fd2f072370ec.bed
- AciCC2_super_enhancer_peaks_5714ac0f2fd6ef3cf59d69d5114356e4.bed
- AciCC3_CTCF_peaks_c611c1d548f65c802f4f88aedba9f768.bed
- AciCC3_H3K27Ac_peaks_97e804349bba944e7d5d1b8ede631466.bed
- AciCC3_H3K27me3_peaks_fb2e726ae020cdbe2aa9512e31ea0d41.bed
- AciCC3_H3K4me3_peaks_f783774d435cce4e7b412c68ec40939d.bed
- AciCC3_NR4A3_peaks_af3ec0dea8c10b071a58b348f9148080.bed
- AciCC3_super_enhancer_peaks_ff95672c1b911065d69046579a65992d.bed
- Parotid_Gland3_CTCF_peaks_651723dd871e8a81ca6890e05137880b.bed
- Parotid_Gland3_H3K27Ac_peaks_126438a74560e776bcf8ec776cdd4640.bed
- Parotid_Gland3_H3K27me3_peaks_a3930e0c6493f6297169e80148ae8fef.bed
- Parotid_Gland3_H3K4me3_peaks_186fc855845537c54dc14bd16821f812.bed
- Parotid_Gland3_NR4A3_peaks_05be8421f1989fd1a9b0a0bbf7cd6a6f.bed
- Parotid_Gland3_super_enhancer_peaks_35c87c26ee2f9666ae6e24b3dd376e68.bed
ChIP-Seq signal files (bigWig format)
- AciCC1_CTCF_chip_signal_7d1b78e4c5ce944e24440dbdfd5b908b.bw
- AciCC1_H3K27Ac_chip_signal_f2cfdda403ecfcf67c0b6045f490137b.bw
- AciCC1_H3K27me3_chip_signal_dfa1a91a9bef6c9b456615e62aa2f951.bw
- AciCC1_H3K4me3_chip_signal_17c9ebe6f38bd5c7d54487752e29c3f5.bw
- AciCC1_NR4A3_chip_signal_c2e112bf5926f70e21d0b278e5f45635.bw
- AciCC2_CTCF_chip_signal_0f3bcab38c4608acd7bd65e39898dae7.bw
- AciCC2_H3K27Ac_chip_signal_f6e037d33b45d599748edd5c8b129e91.bw
- AciCC2_H3K27me3_chip_signal_b4393172fc7b35d55075d61d42b1a429.bw
- AciCC2_H3K4me3_chip_signal_fd7ac24b019113f4947acaf4bd53f12f.bw
- AciCC2_NR4A3_chip_signal_34d46d654f7c7c10856e1a200a9177a4.bw
- AciCC3_CTCF_chip_signal_fb5252020f1773654d5e56a849f2efe3.bw
- AciCC3_H3K27Ac_chip_signal_2ee96af07c5d1e02147b174e6001e462.bw
- AciCC3_H3K27me3_chip_signal_ce6b1014eacea2638df00b35bf0bc9e0.bw
- AciCC3_H3K4me3_chip_signal_382fc8cab2110bff6909a155562e5c2e.bw
- AciCC3_NR4A3_chip_signal_23e1c3d61c68d7b669dab45a545eb5c0.bw
- Parotid_Gland3_CTCF_chip_signal_0a669d678c6a83b7b1cda7ecd6e1fc5b.bw
- Parotid_Gland3_H3K27Ac_chip_signal_a19976272ce5927c945a480276abd635.bw
- Parotid_Gland3_H3K27me3_chip_signal_3090f6a3a4248ad3c80d93e5b3324c37.bw
- Parotid_Gland3_H3K4me3_chip_signal_5392b73b61eb11051b11d4e0a8267221.bw
- Parotid_Gland3_NR4A3_chip_signal_024f8f668cbf06ca7d33763ed17da42a.bw
Methylation call files (bedGraph format)
- AciCC1_methylationCalls_8906b27a616fa5b11eee438f79858517.bedGraph.gz
- AciCC2_methylationCalls_b5e7cd8f983ccd7e8b3655707f49fe79.bedGraph.gz
- AciCC3_methylationCalls_7808c8dc9dc49587e228b0f6171fc91c.bedGraph.gz
- Parotid_Gland1_methylationCalls_966b8f202b698a9ef90d2c6d22621056.bedGraph.gz
- Parotid_Gland2_methylationCalls_cc1afa52f36543bbf82c2776cbffde08.bedGraph.gz
- Parotid_Gland3_methylationCalls_5d74b8d198561823791b010427261a22.bedGraph.gz
RNA-Seq tables Mouse
- count_matrix_mouse.csv
- fpkm_matrix_mouse.csv
RNA-Seq tables Human
- count_matrix_human.csv
- fpkm_matrix_human.csv
Files
count_matrix_human.csv
Files
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Additional details
References
- Haller, F. et al. Enhancer hijacking activates oncogenic transcription factor NR4A3 in acinic cell carcinomas of the salivary glands. Nature Communications 10, 1-13 (2019).