August 4, 2017 Dataset Open Access

Alasoo, Kaur

JSON Export

{
  "files": [
    {
      "links": {
        "self": "https://zenodo.org/api/files/43213fed-09c5-4335-aa0e-e2ee972fc854/naive_vs_IFNg_DESeq2_fold_change.txt.gz"
      }, 
      "checksum": "md5:d30c466506cf7b6cb784ced7a9e4a68d", 
      "bucket": "43213fed-09c5-4335-aa0e-e2ee972fc854", 
      "key": "naive_vs_IFNg_DESeq2_fold_change.txt.gz", 
      "type": "gz", 
      "size": 1701488
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/43213fed-09c5-4335-aa0e-e2ee972fc854/naive_vs_IFNg%2BSalmonella_DESeq2_fold_change.txt.gz"
      }, 
      "checksum": "md5:5dfbed8bf82addcc42b8bba8f40f0a19", 
      "bucket": "43213fed-09c5-4335-aa0e-e2ee972fc854", 
      "key": "naive_vs_IFNg+Salmonella_DESeq2_fold_change.txt.gz", 
      "type": "gz", 
      "size": 1694658
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/43213fed-09c5-4335-aa0e-e2ee972fc854/naive_vs_Salmonella_DESeq2_fold_change.txt.gz"
      }, 
      "checksum": "md5:3fa2cf63753e72e1f5c884b9bcb1235c", 
      "bucket": "43213fed-09c5-4335-aa0e-e2ee972fc854", 
      "key": "naive_vs_Salmonella_DESeq2_fold_change.txt.gz", 
      "type": "gz", 
      "size": 1696396
    }
  ], 
  "owners": [
    11899
  ], 
  "doi": "10.5281/zenodo.839011", 
  "stats": {
    "version_unique_downloads": 12.0, 
    "unique_views": 60.0, 
    "views": 61.0, 
    "version_views": 61.0, 
    "unique_downloads": 13.0, 
    "version_unique_views": 60.0, 
    "volume": 54326658.0, 
    "version_downloads": 30.0, 
    "downloads": 32.0, 
    "version_volume": 50930512.0
  }, 
  "links": {
    "doi": "https://doi.org/10.5281/zenodo.839011", 
    "conceptdoi": "https://doi.org/10.5281/zenodo.839010", 
    "bucket": "https://zenodo.org/api/files/43213fed-09c5-4335-aa0e-e2ee972fc854", 
    "conceptbadge": "https://zenodo.org/badge/doi/10.5281/zenodo.839010.svg", 
    "html": "https://zenodo.org/record/839011", 
    "latest_html": "https://zenodo.org/record/839011", 
    "badge": "https://zenodo.org/badge/doi/10.5281/zenodo.839011.svg", 
    "latest": "https://zenodo.org/api/records/839011"
  }, 
  "conceptdoi": "10.5281/zenodo.839010", 
  "created": "2017-08-04T15:36:35.681051+00:00", 
  "updated": "2020-01-24T19:24:24.321818+00:00", 
  "conceptrecid": "839010", 
  "revision": 5, 
  "id": 839011, 
  "metadata": {
    "access_right_category": "success", 
    "doi": "10.5281/zenodo.839011", 
    "description": "<p>We used likelihood ratio test implemented in DESeq2 v1.10.0 (test = \u201cLRT\u201d) to test if a model that allowed different mean expression in each condition explained the data better than a null model assuming the same mean expression across conditions. See the manuscript for more details:\u00a0http://www.biorxiv.org/content/early/2017/05/18/102392 .</p>\n\n<p>We used the following commands in DESeq2:<br>\n#Run DESeq2<br>\ndds = DESeq2::DESeqDataSetFromMatrix(combined_expression_data_filtered$counts, design, ~condition_name)\u00a0<br>\ndds = DESeq2::DESeq(dds, test = \"LRT\", reduced = ~ 1)</p>\n\n<p>#Extract differentially expressed genes in each condition<br>\nifng_genes = results(dds, contrast=c(\"condition_name\",\"IFNg\",\"naive\"))\u00a0<br>\nsl1344_genes = results(dds, contrast=c(\"condition_name\",\"SL1344\",\"naive\"))\u00a0<br>\nifng_sl1344_genes = results(dds, contrast=c(\"condition_name\",\"IFNg_SL1344\",\"naive\"))</p>", 
    "license": {
      "id": "CC-BY-4.0"
    }, 
    "title": "Differential gene expression in iPSC-derived macrophages after IFNg stimulation and Salmonella infection", 
    "relations": {
      "version": [
        {
          "count": 1, 
          "index": 0, 
          "parent": {
            "pid_type": "recid", 
            "pid_value": "839010"
          }, 
          "is_last": true, 
          "last_child": {
            "pid_type": "recid", 
            "pid_value": "839011"
          }
        }
      ]
    }, 
    "communities": [
      {
        "id": "macrophage-gene-expression-genetics"
      }
    ], 
    "keywords": [
      "RNA-seq", 
      "differential expression"
    ], 
    "publication_date": "2017-08-04", 
    "creators": [
      {
        "affiliation": "Wellcome Trust Sanger Institute", 
        "name": "Alasoo, Kaur"
      }
    ], 
    "access_right": "open", 
    "resource_type": {
      "type": "dataset", 
      "title": "Dataset"
    }, 
    "related_identifiers": [
      {
        "scheme": "doi", 
        "identifier": "10.5281/zenodo.839010", 
        "relation": "isVersionOf"
      }
    ]
  }
}