{
"@context": "/terms/",
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"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2774OLAH",
"aliases": [
"jay-shendure:analysis_set_scQers_mEBs"
],
"assay_titles": [
"MPRA (scQer)"
],
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing file format specifications",
"detail": "Tabular file [IGVFFI2410QRVN](/tabular-files/IGVFFI2410QRVN/) has no `file_format_specifications`. Tabular files are expected to link to a file format specifications document describing the headers of the file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_tabular_file_no_file_format_specifications",
"path": "/tabular-files/IGVFFI2410QRVN/"
}
],
"WARNING": [
{
"category": "missing analysis step version",
"detail": "Analysis set [IGVFDS2774OLAH](/analysis-sets/IGVFDS2774OLAH/) links to file(s) [IGVFFI2410QRVN](/tabular-files/IGVFFI2410QRVN/) that are missing `analysis_step_version`. Analysis set files are expected to specify analysis step version.",
"level": 40,
"level_name": "WARNING",
"name": "audit_analysis_set_files_missing_analysis_step_version",
"path": "/analysis-sets/IGVFDS2774OLAH/"
}
]
},
"award": {
"@id": "/awards/HG011966/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/eb543cda-67b7-493c-84eb-187d0dac13ba/",
"title": "Jay Shendure"
},
"title": "Massively parallel characterization of variants and elements impacting transcriptional regulation in dynamic cellular systems"
},
"control_for": [],
"creation_timestamp": "2023-12-12T23:07:37.491245+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO3898MNLZ/",
"accession": "IGVFDO3898MNLZ",
"aliases": [
"jay-shendure:WD44_donor"
],
"sex": "male",
"status": "released",
"taxa": "Mus musculus"
}
],
"file_set_type": "principal analysis",
"files": [
{
"@id": "/tabular-files/IGVFFI2410QRVN/",
"accession": "IGVFFI2410QRVN",
"aliases": [
"jay-shendure:tabularfile_CREs_scQers-processed_LaLanne"
],
"content_type": "element quantifications",
"creation_timestamp": "2024-05-07T19:52:36.459604+00:00",
"file_format": "tsv",
"file_size": 17966180,
"href": "/tabular-files/IGVFFI2410QRVN/@@download/IGVFFI2410QRVN.tsv.gz",
"s3_uri": "s3://igvf-files/2024/05/07/c81b696f-9e81-4c58-8e59-64ce9894c005/IGVFFI2410QRVN.txt.gz",
"submitted_file_name": "/net/shendure/vol10/projects/JBL/IGVF_for_Beth_nobackup/assigned_oBC_CRE_mBC_joined_counts_sc_rep_mEB_series.txt.gz",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_set_for": [],
"input_file_sets": [
{
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"accession": "IGVFDS0238EDXB",
"aliases": [
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],
"file_set_type": "elements"
},
{
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],
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},
{
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],
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},
{
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],
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},
{
"@id": "/measurement-sets/IGVFDS7984TCLH/",
"accession": "IGVFDS7984TCLH",
"aliases": [
"jay-shendure:dev_CRE_mEBs_GEx_repB_10Xlane2_reads"
],
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},
{
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],
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},
{
"@id": "/measurement-sets/IGVFDS1598IBNK/",
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"aliases": [
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},
{
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],
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},
{
"@id": "/auxiliary-sets/IGVFDS8622RRUW/",
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],
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},
{
"@id": "/auxiliary-sets/IGVFDS7168JGPF/",
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],
"file_set_type": "quantification DNA barcode sequencing"
},
{
"@id": "/auxiliary-sets/IGVFDS1166KGZN/",
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],
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},
{
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"jay-shendure:dev_CRE_mEBs_mBC_rep2B_10Xlane1_reads"
],
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},
{
"@id": "/auxiliary-sets/IGVFDS7645MEIE/",
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"jay-shendure:dev_CRE_mEBs_mBC_rep2B_10Xlane2_reads"
],
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},
{
"@id": "/auxiliary-sets/IGVFDS7792HFAY/",
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],
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},
{
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],
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},
{
"@id": "/auxiliary-sets/IGVFDS1156NHWQ/",
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],
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},
{
"@id": "/auxiliary-sets/IGVFDS8758JSUK/",
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"aliases": [
"jay-shendure:dev_CRE_mEBs_oBC_repB_10Xlane2_reads"
],
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},
{
"@id": "/auxiliary-sets/IGVFDS6059ISIJ/",
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"aliases": [
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],
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},
{
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],
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}
],
"lab": {
"@id": "/labs/jay-shendure/",
"title": "Jay Shendure, UW"
},
"notes": "This object's file_set_type was primary analysis and has been updated to be principal analysis.",
"protocols": [
"https://www.protocols.io/file/n92rb7r27.pdf"
],
"publications": [
{
"@id": "/publications/398edd7f-1ebb-40a0-a04b-450a2565667c/",
"publication_identifiers": [
"doi:10.1038/s41592-024-02260-3",
"PMID:38724692"
]
}
],
"release_timestamp": "2024-06-27T00:41:44.404495+00:00",
"sample_summary": "mouse embryonic stem cell differentiated cell specimen induced to embryoid body, at 1 time point(s) post change, modified with a reporter library",
"samples": [
{
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],
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"Item"
],
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"targeted_sample_term": {
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{
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],
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{
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],
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}
],
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},
{
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],
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],
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},
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],
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},
{
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"Sample",
"Item"
],
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{
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],
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}
],
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"targeted_sample_term": {
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},
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}
],
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"submitted_by": {
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"title": "Beth Martin"
},
"submitted_files_timestamp": "2024-05-07T19:52:36.459604+00:00",
"summary": "principal analysis of MPRA (scQer) data",
"uuid": "85b28f63-a08e-495e-b610-5a2068e600a6"
}