{
"@context": "/terms/",
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"@type": [
"TabularFile",
"File",
"Item"
],
"accession": "IGVFFI2013BVRU",
"aliases": [
"ansuman-satpathy:igvf12_fragments_10x2"
],
"analysis_step_version": "/analysis-step-versions/4e4a3f0b-c3bc-477c-bc53-c3091bc56756/",
"assay_titles": [
"10x multiome with MULTI-seq"
],
"audit": {},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization"
},
"barcode_map_for": [],
"checkfiles_version": "v14",
"content_md5sum": "c8048f25707c82a9c5b277a449176865",
"content_type": "fragments",
"controlled_access": true,
"creation_timestamp": "2025-01-28T06:11:30.209337+00:00",
"derived_from": [
"/sequence-files/IGVFFI1713PZKF/",
"/sequence-files/IGVFFI1675JYIK/",
"/sequence-files/IGVFFI5791ZCZX/",
"/sequence-files/IGVFFI1858ZMBL/",
"/sequence-files/IGVFFI8803NWUY/",
"/sequence-files/IGVFFI5739MQHP/",
"/sequence-files/IGVFFI1533MLGF/",
"/sequence-files/IGVFFI4035TVYA/",
"/sequence-files/IGVFFI8127WKJW/",
"/sequence-files/IGVFFI5994KKRZ/",
"/sequence-files/IGVFFI2221QTKE/",
"/sequence-files/IGVFFI8152JUHC/",
"/sequence-files/IGVFFI9939CNBA/",
"/sequence-files/IGVFFI1317ZWHM/",
"/sequence-files/IGVFFI0308JCQR/",
"/sequence-files/IGVFFI4141LYRL/",
"/sequence-files/IGVFFI7630GWQL/",
"/sequence-files/IGVFFI9185DYIT/",
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"/sequence-files/IGVFFI7357JFWG/",
"/sequence-files/IGVFFI1663BYDQ/",
"/sequence-files/IGVFFI4087LAFL/",
"/sequence-files/IGVFFI8435FWOI/",
"/sequence-files/IGVFFI5239RCCT/",
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],
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"file_format_specifications": [
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],
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"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4931IGGD",
"file_set_type": "intermediate analysis",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM5189FTFS/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM5189FTFS",
"classifications": [
"differentiated cell specimen",
"tissue",
"multiplexed sample"
],
"disease_terms": [],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000236/",
"status": "released",
"term_name": "B cell"
},
{
"@id": "/sample-terms/UBERON_0002371/",
"status": "released",
"term_name": "bone marrow"
}
],
"status": "released",
"summary": "multiplexed sample: Homo sapiens (female) B differentiated cell specimen induced to plasmablast for 6 days; Homo sapiens (female) B differentiated cell specimen induced to plasmablast for 5 days; ... and 10 more samples",
"taxa": "Homo sapiens",
"treatments": []
}
],
"status": "released",
"summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix"
},
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"gene_list_for": [],
"href": "/tabular-files/IGVFFI2013BVRU/@@download/IGVFFI2013BVRU.tsv.gz",
"input_file_for": [
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],
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"lab": {
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"title": "Ansuman Satpathy, Stanford"
},
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"md5sum": "a447eeabf30c20e631e724bdb1cfea64",
"notes": "File has # in headers, the current version of checkfiles does not allow for that but this is a valid file output from cell ranger. Therefore, we have patched the upload_status to \"validation exempted\"",
"quality_metrics": [],
"release_timestamp": "2025-03-22T00:43:09.929307+00:00",
"s3_uri": "s3://igvf-restricted-files/2025/01/28/84f71f7d-d094-4da1-aef5-e03d05850d73/IGVFFI2013BVRU.tsv.gz",
"schema_version": "15",
"status": "released",
"submitted_by": {
"@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
"title": "Christopher Mcginnis"
},
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf12/e12l2_fragments.tsv.gz",
"summary": "fragments",
"upload_status": "validation exempted",
"uuid": "84f71f7d-d094-4da1-aef5-e03d05850d73",
"validation_error_detail": "{\"tabular_file_error\": {\"schema\": null, \"error_number_limit\": 1000, \"number_of_errors\": 1000, \"extra-cell\": {\"count\": 1000, \"description\": \"This row has more values compared to the header row (the first row in the data source). A key concept is that all the rows in tabular data must have the same number of columns.\", \"details\": [{\"row_number\": 52, \"field_number\": 2, \"note\": \"\"}, {\"row_number\": 52, \"field_number\": 3, \"note\": \"\"}]}, \"error_types\": [\"extra-cell\"]}}",
"workflow": {
"@id": "/workflows/IGVFWF1453HVEC/",
"name": "Satpathy Cell Ranger",
"uniform_pipeline": false
}
}