{
"@context": "/terms/",
"@id": "/tabular-files/IGVFFI0627MDWY/",
"@type": [
"TabularFile",
"File",
"Item"
],
"accession": "IGVFFI0627MDWY",
"aliases": [
"ansuman-satpathy:igvf10_fragments_10x1"
],
"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": "444f858186582fc52618b75a975a0605",
"content_type": "fragments",
"controlled_access": false,
"creation_timestamp": "2025-01-28T06:04:23.579216+00:00",
"derived_from": [
"/sequence-files/IGVFFI1562OZKE/",
"/sequence-files/IGVFFI6421BIVI/",
"/sequence-files/IGVFFI5662ZYXD/",
"/sequence-files/IGVFFI4218WPJB/",
"/sequence-files/IGVFFI9550CRCV/",
"/sequence-files/IGVFFI0859TDIG/",
"/sequence-files/IGVFFI8243RHWY/",
"/sequence-files/IGVFFI5047YIPF/"
],
"file_format": "tsv",
"file_format_specifications": [
"/documents/43920105-5f77-430a-9bcd-f00180ff2b1d/"
],
"file_set": {
"@id": "/analysis-sets/IGVFDS2018URDY/",
"accession": "IGVFDS2018URDY",
"file_set_type": "intermediate analysis",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM0539NUPM/",
"accession": "IGVFSM0539NUPM",
"classifications": [
"cell line",
"multiplexed sample"
],
"disease_terms": [],
"modifications": [
{
"@id": "/crispr-modifications/b4bc725a-8eeb-4180-9789-bece3516c0c1/",
"modality": "interference",
"status": "released",
"summary": "CRISPRi Sp-dCas9-KOX1-KRAB"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"status": "released",
"term_name": "THP-1"
},
{
"@id": "/sample-terms/EFO_0002067/",
"status": "released",
"term_name": "K562"
},
{
"@id": "/sample-terms/EFO_0002796/",
"status": "released",
"term_name": "Jurkat"
},
{
"@id": "/sample-terms/NTR_0000753/",
"status": "released",
"term_name": "TeloHAEC"
}
],
"status": "released",
"summary": "multiplexed sample: Jurkat cell line, male, Homo sapiens treated with 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours; K562 cell line, female, Homo sapiens modified with CRISPRi Sp-dCas9-KOX1-KRAB; ... and 8 more samples",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/42b3c61d-38de-4bd2-bb39-33c125a417cb/",
"purpose": "stimulation",
"status": "released",
"summary": "Treatment of 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours",
"treatment_term_name": "phorbol 13-acetate 12-myristate"
},
{
"@id": "/treatments/df02c0d4-f796-4f77-bfbc-388cdbfcc615/",
"purpose": "stimulation",
"status": "released",
"summary": "Treatment of 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours",
"treatment_term_name": "T-cell surface glycoprotein CD3 gamma chain"
}
]
},
{
"@id": "/multiplexed-samples/IGVFSM4547BFMA/",
"accession": "IGVFSM4547BFMA",
"classifications": [
"cell line",
"multiplexed sample"
],
"disease_terms": [],
"modifications": [
{
"@id": "/crispr-modifications/b4bc725a-8eeb-4180-9789-bece3516c0c1/",
"modality": "interference",
"status": "released",
"summary": "CRISPRi Sp-dCas9-KOX1-KRAB"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"status": "released",
"term_name": "THP-1"
},
{
"@id": "/sample-terms/EFO_0002067/",
"status": "released",
"term_name": "K562"
},
{
"@id": "/sample-terms/EFO_0002796/",
"status": "released",
"term_name": "Jurkat"
},
{
"@id": "/sample-terms/NTR_0000753/",
"status": "released",
"term_name": "TeloHAEC"
}
],
"status": "released",
"summary": "multiplexed sample: Jurkat cell line, male, Homo sapiens treated with 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours; K562 cell line, female, Homo sapiens modified with CRISPRi Sp-dCas9-KOX1-KRAB; ... and 8 more samples",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/42b3c61d-38de-4bd2-bb39-33c125a417cb/",
"purpose": "stimulation",
"status": "released",
"summary": "Treatment of 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours",
"treatment_term_name": "phorbol 13-acetate 12-myristate"
},
{
"@id": "/treatments/df02c0d4-f796-4f77-bfbc-388cdbfcc615/",
"purpose": "stimulation",
"status": "released",
"summary": "Treatment of 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours",
"treatment_term_name": "T-cell surface glycoprotein CD3 gamma chain"
}
]
}
],
"status": "released",
"summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix"
},
"file_size": 7834091145,
"gene_list_for": [],
"href": "/tabular-files/IGVFFI0627MDWY/@@download/IGVFFI0627MDWY.tsv.gz",
"input_file_for": [
"/index-files/IGVFFI3930OIYP/",
"/tabular-files/IGVFFI8318PQLH/"
],
"integrated_in": [],
"lab": {
"@id": "/labs/ansuman-satpathy/",
"title": "Ansuman Satpathy, Stanford"
},
"loci_list_for": [],
"md5sum": "c69fb4ea81ca5efb0834a597ffe6e12c",
"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": "2025-03-07T06:04:56.379355+00:00",
"s3_uri": "s3://igvf-files/2025/01/28/c9327329-e14b-4d32-a5ca-d5244c913121/IGVFFI0627MDWY.tsv.gz",
"schema_version": "13",
"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/igvf10/e10l1_fragments.tsv.gz",
"summary": "fragments",
"upload_status": "validation exempted",
"uuid": "c9327329-e14b-4d32-a5ca-d5244c913121",
"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
}
}