{
"@context": "/terms/",
"@id": "/tabular-files/IGVFFI4750SIPG/",
"@type": [
"TabularFile",
"File",
"Item"
],
"accession": "IGVFFI4750SIPG",
"aliases": [
"ansuman-satpathy:igvf1_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": "34930345e6acc3235804073d96ff1d18",
"content_type": "fragments",
"controlled_access": false,
"creation_timestamp": "2025-01-28T05:49:12.765264+00:00",
"derived_from": [
"/sequence-files/IGVFFI4807KWFS/",
"/sequence-files/IGVFFI5304CPDI/",
"/sequence-files/IGVFFI0737RLFI/",
"/sequence-files/IGVFFI0660RPDV/",
"/sequence-files/IGVFFI8458QQVB/",
"/sequence-files/IGVFFI7273QKAQ/",
"/sequence-files/IGVFFI3023ETQK/",
"/sequence-files/IGVFFI4221MLSD/"
],
"file_format": "tsv",
"file_format_specifications": [
"/documents/43920105-5f77-430a-9bcd-f00180ff2b1d/"
],
"file_set": {
"@id": "/analysis-sets/IGVFDS8205NXKP/",
"accession": "IGVFDS8205NXKP",
"file_set_type": "intermediate analysis",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM4662QKFQ/",
"accession": "IGVFSM4662QKFQ",
"classifications": [
"cell line",
"multiplexed sample"
],
"disease_terms": [],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002067/",
"status": "released",
"term_name": "K562"
},
{
"@id": "/sample-terms/EFO_0002793/",
"status": "released",
"term_name": "HL-60"
},
{
"@id": "/sample-terms/EFO_0002869/",
"status": "released",
"term_name": "U2OS"
},
{
"@id": "/sample-terms/EFO_0007598/",
"status": "released",
"term_name": "HAP-1"
},
{
"@id": "/sample-terms/EFO_0022838/",
"status": "released",
"term_name": "HUDEP-2"
}
],
"status": "released",
"summary": "multiplexed sample: HAP-1 cell line, male, Homo sapiens; HAP-1 cell line, male, Homo sapiens; ... and 13 more samples",
"taxa": "Homo sapiens",
"treatments": []
},
{
"@id": "/multiplexed-samples/IGVFSM8645VILQ/",
"accession": "IGVFSM8645VILQ",
"classifications": [
"cell line",
"multiplexed sample"
],
"disease_terms": [],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002067/",
"status": "released",
"term_name": "K562"
},
{
"@id": "/sample-terms/EFO_0002793/",
"status": "released",
"term_name": "HL-60"
},
{
"@id": "/sample-terms/EFO_0002869/",
"status": "released",
"term_name": "U2OS"
},
{
"@id": "/sample-terms/EFO_0007598/",
"status": "released",
"term_name": "HAP-1"
},
{
"@id": "/sample-terms/EFO_0022838/",
"status": "released",
"term_name": "HUDEP-2"
}
],
"status": "released",
"summary": "multiplexed sample: HAP-1 cell line, male, Homo sapiens; HAP-1 cell line, male, Homo sapiens; ... and 13 more samples",
"taxa": "Homo sapiens",
"treatments": []
}
],
"status": "released",
"summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix"
},
"file_size": 4048332324,
"gene_list_for": [],
"href": "/tabular-files/IGVFFI4750SIPG/@@download/IGVFFI4750SIPG.tsv.gz",
"input_file_for": [
"/index-files/IGVFFI9225UJLT/",
"/tabular-files/IGVFFI0034FSXI/"
],
"integrated_in": [],
"lab": {
"@id": "/labs/ansuman-satpathy/",
"title": "Ansuman Satpathy, Stanford"
},
"loci_list_for": [],
"md5sum": "ce69e8dd1524f7f57da960273d09fe35",
"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": "2025-03-07T06:04:07.033657+00:00",
"s3_uri": "s3://igvf-files/2025/01/28/f4e54b3f-1d07-4ce7-8b5b-24f3646c16bd/IGVFFI4750SIPG.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/igvf1/e1l2_fragments.tsv.gz",
"summary": "fragments",
"upload_status": "validation exempted",
"uuid": "f4e54b3f-1d07-4ce7-8b5b-24f3646c16bd",
"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
}
}