{
"@context": "/terms/",
"@id": "/tabular-files/IGVFFI5550IBSN/",
"@type": [
"TabularFile",
"File",
"Item"
],
"accession": "IGVFFI5550IBSN",
"aliases": [
"ansuman-satpathy:igvf11_fragments_10x4"
],
"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": "42c5739c39318c4b29ae8b56a1f0bb1b",
"content_type": "fragments",
"controlled_access": false,
"creation_timestamp": "2025-01-28T06:09:06.805772+00:00",
"derived_from": [
"/sequence-files/IGVFFI6345HQKI/",
"/sequence-files/IGVFFI6518WZLR/",
"/sequence-files/IGVFFI2350QBEI/",
"/sequence-files/IGVFFI1167LMYO/",
"/sequence-files/IGVFFI7980SPCZ/",
"/sequence-files/IGVFFI2600SVRW/",
"/sequence-files/IGVFFI7782QPFL/",
"/sequence-files/IGVFFI2420PDXE/",
"/sequence-files/IGVFFI9915FQPN/",
"/sequence-files/IGVFFI5928GUSU/",
"/sequence-files/IGVFFI1725EZEV/",
"/sequence-files/IGVFFI1639RTNK/",
"/sequence-files/IGVFFI5757ZDOL/",
"/sequence-files/IGVFFI8516KCXK/",
"/sequence-files/IGVFFI4911YVMQ/",
"/sequence-files/IGVFFI1664PYFR/"
],
"file_format": "tsv",
"file_format_specifications": [
"/documents/43920105-5f77-430a-9bcd-f00180ff2b1d/"
],
"file_set": {
"@id": "/analysis-sets/IGVFDS8136ENRY/",
"accession": "IGVFDS8136ENRY",
"file_set_type": "intermediate analysis",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM9367PJMT/",
"accession": "IGVFSM9367PJMT",
"classifications": [
"differentiated cell specimen",
"multiplexed sample"
],
"disease_terms": [],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0005904/",
"status": "released",
"term_name": "H7-hESC"
},
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "released",
"summary": "multiplexed sample: H7-hESC differentiated cell specimen, female, Homo sapiens; GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 6 days, male, Homo sapiens; ... and 10 more samples",
"taxa": "Homo sapiens",
"treatments": []
},
{
"@id": "/multiplexed-samples/IGVFSM9487HFQW/",
"accession": "IGVFSM9487HFQW",
"classifications": [
"differentiated cell specimen",
"multiplexed sample"
],
"disease_terms": [],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0005904/",
"status": "released",
"term_name": "H7-hESC"
},
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "released",
"summary": "multiplexed sample: H7-hESC differentiated cell specimen, female, Homo sapiens; GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 6 days, male, Homo sapiens; ... and 10 more samples",
"taxa": "Homo sapiens",
"treatments": []
},
{
"@id": "/multiplexed-samples/IGVFSM8200CKYL/",
"accession": "IGVFSM8200CKYL",
"classifications": [
"differentiated cell specimen",
"multiplexed sample"
],
"disease_terms": [],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0005904/",
"status": "released",
"term_name": "H7-hESC"
},
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "released",
"summary": "multiplexed sample: H7-hESC differentiated cell specimen, female, Homo sapiens; GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 6 days, male, Homo sapiens; ... and 10 more samples",
"taxa": "Homo sapiens",
"treatments": []
},
{
"@id": "/multiplexed-samples/IGVFSM6160ZDRZ/",
"accession": "IGVFSM6160ZDRZ",
"classifications": [
"differentiated cell specimen",
"multiplexed sample"
],
"disease_terms": [],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0005904/",
"status": "released",
"term_name": "H7-hESC"
},
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "released",
"summary": "multiplexed sample: H7-hESC differentiated cell specimen, female, Homo sapiens; GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 6 days, male, Homo sapiens; ... 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"
},
"file_size": 3617611116,
"gene_list_for": [],
"href": "/tabular-files/IGVFFI5550IBSN/@@download/IGVFFI5550IBSN.tsv.gz",
"input_file_for": [
"/index-files/IGVFFI9936KULB/",
"/tabular-files/IGVFFI8715YPRJ/"
],
"integrated_in": [],
"lab": {
"@id": "/labs/ansuman-satpathy/",
"title": "Ansuman Satpathy, Stanford"
},
"loci_list_for": [],
"md5sum": "03c5dec578f00209135f9d61e3e38022",
"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": "2025-03-07T06:05:03.983319+00:00",
"s3_uri": "s3://igvf-files/2025/01/28/2b2435ba-8d94-4881-9b3d-307612d89645/IGVFFI5550IBSN.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/igvf11/e11l4_fragments.tsv.gz",
"summary": "fragments",
"upload_status": "validation exempted",
"uuid": "2b2435ba-8d94-4881-9b3d-307612d89645",
"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
}
}