{
"@context": "/terms/",
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"@type": [
"TabularFile",
"File",
"Item"
],
"accession": "IGVFFI7268PNWE",
"aliases": [
"ansuman-satpathy:igvf4_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": "2c70f3fcc95d95cc815ca2b60383e01b",
"content_type": "fragments",
"controlled_access": false,
"creation_timestamp": "2025-01-28T05:53:19.868552+00:00",
"derived_from": [
"/sequence-files/IGVFFI7313NUEB/",
"/sequence-files/IGVFFI2036ECMB/",
"/sequence-files/IGVFFI6631RXKI/",
"/sequence-files/IGVFFI0104HBOM/",
"/sequence-files/IGVFFI3571ZWPJ/",
"/sequence-files/IGVFFI8805HERJ/",
"/sequence-files/IGVFFI7329CJCL/",
"/sequence-files/IGVFFI8315YWHU/"
],
"file_format": "tsv",
"file_format_specifications": [
"/documents/43920105-5f77-430a-9bcd-f00180ff2b1d/"
],
"file_set": {
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"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3751NDQI",
"file_set_type": "intermediate analysis",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM7068ZFMY/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM7068ZFMY",
"classifications": [
"cell line",
"multiplexed sample"
],
"disease_terms": [],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "released",
"summary": "multiplexed sample: Homo sapiens (male) GM25256 (WTC-11) cell line treated with 50 ng/mL interleukin 4 for 1 day; Homo sapiens (male) GM25256 (WTC-11) cell line treated with 100 ng/mL macrophage colony-stimulating factor 1 for 7 days; ... and 13 more samples",
"taxa": "Homo sapiens",
"treatments": [
{
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"purpose": "differentiation",
"status": "in progress",
"summary": "Treatment of 0.025 ng/mL acetylated low density lipoprotein for 1 day",
"treatment_term_name": "acetylated low density lipoprotein"
},
{
"@id": "/treatments/729630f8-aa05-47f5-9cba-ee7a264da593/",
"purpose": "differentiation",
"status": "in progress",
"summary": "Treatment of 50 ng/mL interleukin 4 for 1 day",
"treatment_term_name": "interleukin 4"
},
{
"@id": "/treatments/ae8065d2-85f3-498e-b4f2-01a38756d48e/",
"purpose": "differentiation",
"status": "in progress",
"summary": "Treatment of 20 ng/mL interferon gamma for 1 day",
"treatment_term_name": "interferon gamma"
},
{
"@id": "/treatments/bec71d5e-97ef-489a-acb7-5336691b6c39/",
"purpose": "differentiation",
"status": "in progress",
"summary": "Treatment of 100 ng/mL macrophage colony-stimulating factor 1 for 7 days",
"treatment_term_name": "macrophage colony-stimulating factor 1"
}
]
}
],
"status": "released",
"summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix"
},
"file_size": 6809536486,
"gene_list_for": [],
"href": "/tabular-files/IGVFFI7268PNWE/@@download/IGVFFI7268PNWE.tsv.gz",
"input_file_for": [
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],
"integrated_in": [],
"lab": {
"@id": "/labs/ansuman-satpathy/",
"title": "Ansuman Satpathy, Stanford"
},
"loci_list_for": [],
"md5sum": "f46d540ae8ed8401ec52482ef48ec081",
"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": "2025-03-07T06:04:24.881556+00:00",
"s3_uri": "s3://igvf-files/2025/01/28/e6baa73c-ab12-4c54-9194-f64e327e1fc1/IGVFFI7268PNWE.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/igvf4/e4l2_fragments.tsv.gz",
"summary": "fragments",
"upload_status": "validation exempted",
"uuid": "e6baa73c-ab12-4c54-9194-f64e327e1fc1",
"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
}
}