{
"@context": "/terms/",
"@id": "/matrix-files/IGVFFI8511XOAV/",
"@type": [
"MatrixFile",
"File",
"Item"
],
"accession": "IGVFFI8511XOAV",
"aliases": [
"ansuman-satpathy:igvf17_raw_rna_counts_10x4"
],
"analysis_step_version": "/analysis-step-versions/072beaf9-db5c-4bb3-9d63-e5cf7ee29dd6/",
"assay_titles": [
"10x multiome with MULTI-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI8511XOAV](/matrix-files/IGVFFI8511XOAV/) has in progress subobject reference file [IGVFFI3944QOJF](/reference-files/IGVFFI3944QOJF/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI8511XOAV/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI8511XOAV](/matrix-files/IGVFFI8511XOAV/) has in progress subobject reference file [IGVFFI8311QXYM](/reference-files/IGVFFI8311QXYM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI8511XOAV/"
}
]
},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization"
},
"checkfiles_version": "v14",
"content_summary": "cell by gene in raw feature barcode matrix",
"content_type": "raw feature barcode matrix",
"creation_timestamp": "2025-01-28T23:11:51.788936+00:00",
"derived_from": [
"/sequence-files/IGVFFI4582RUSA/",
"/sequence-files/IGVFFI1076NVIH/",
"/sequence-files/IGVFFI7133BHFZ/",
"/sequence-files/IGVFFI2690MYQF/",
"/sequence-files/IGVFFI7108OWMP/",
"/sequence-files/IGVFFI1240VNKQ/",
"/sequence-files/IGVFFI6271BZLD/",
"/sequence-files/IGVFFI7598TGFL/",
"/sequence-files/IGVFFI1115MCGP/",
"/sequence-files/IGVFFI8735GPEL/",
"/sequence-files/IGVFFI0262MIVJ/",
"/sequence-files/IGVFFI0978CLLR/",
"/sequence-files/IGVFFI7374OCNF/",
"/sequence-files/IGVFFI7951TRNJ/",
"/sequence-files/IGVFFI9066SKTV/",
"/sequence-files/IGVFFI7934ZMBN/"
],
"file_format": "hdf5",
"file_format_specifications": [
"/documents/e18648f3-63a8-47e0-be86-2670f0cb68f0/"
],
"file_set": {
"@id": "/analysis-sets/IGVFDS0398ALPE/",
"accession": "IGVFDS0398ALPE",
"file_set_type": "intermediate analysis",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM7909ETQJ/",
"accession": "IGVFSM7909ETQJ",
"classifications": [
"differentiated cell specimen",
"multiplexed sample"
],
"disease_terms": [],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009320/",
"status": "released",
"term_name": "RUES2"
}
],
"status": "released",
"summary": "multiplexed sample: RUES2 differentiated cell specimen induced to gastrula for 2 days, female, Homo sapiens; RUES2 differentiated cell specimen induced to gastrula for 1 day, female, Homo sapiens; ... and 10 more samples",
"taxa": "Homo sapiens",
"treatments": []
},
{
"@id": "/multiplexed-samples/IGVFSM6345RLEH/",
"accession": "IGVFSM6345RLEH",
"classifications": [
"differentiated cell specimen",
"multiplexed sample"
],
"disease_terms": [],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009320/",
"status": "released",
"term_name": "RUES2"
}
],
"status": "released",
"summary": "multiplexed sample: RUES2 differentiated cell specimen induced to gastrula for 2 days, female, Homo sapiens; RUES2 differentiated cell specimen induced to gastrula for 1 day, female, Homo sapiens; ... and 10 more samples",
"taxa": "Homo sapiens",
"treatments": []
},
{
"@id": "/multiplexed-samples/IGVFSM0198VBOA/",
"accession": "IGVFSM0198VBOA",
"classifications": [
"differentiated cell specimen",
"multiplexed sample"
],
"disease_terms": [],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009320/",
"status": "released",
"term_name": "RUES2"
}
],
"status": "released",
"summary": "multiplexed sample: RUES2 differentiated cell specimen induced to gastrula for 2 days, female, Homo sapiens; RUES2 differentiated cell specimen induced to gastrula for 1 day, female, Homo sapiens; ... and 10 more samples",
"taxa": "Homo sapiens",
"treatments": []
},
{
"@id": "/multiplexed-samples/IGVFSM9149ZACE/",
"accession": "IGVFSM9149ZACE",
"classifications": [
"differentiated cell specimen",
"multiplexed sample"
],
"disease_terms": [],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009320/",
"status": "released",
"term_name": "RUES2"
}
],
"status": "released",
"summary": "multiplexed sample: RUES2 differentiated cell specimen induced to gastrula for 2 days, female, Homo sapiens; RUES2 differentiated cell specimen induced to gastrula for 1 day, female, Homo sapiens; ... and 10 more samples",
"taxa": "Homo sapiens",
"treatments": []
},
{
"@id": "/multiplexed-samples/IGVFSM8270UYGU/",
"accession": "IGVFSM8270UYGU",
"classifications": [
"differentiated cell specimen",
"multiplexed sample"
],
"disease_terms": [],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009320/",
"status": "released",
"term_name": "RUES2"
}
],
"status": "released",
"summary": "multiplexed sample: RUES2 differentiated cell specimen induced to gastrula for 2 days, female, Homo sapiens; RUES2 differentiated cell specimen induced to gastrula for 1 day, female, 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": 135556361,
"gene_list_for": [],
"href": "/matrix-files/IGVFFI8511XOAV/@@download/IGVFFI8511XOAV.h5",
"input_file_for": [],
"integrated_in": [],
"lab": {
"@id": "/labs/ansuman-satpathy/",
"title": "Ansuman Satpathy, Stanford"
},
"loci_list_for": [],
"md5sum": "c161ad112704a6044cca702f0f5cda32",
"principal_dimension": "cell",
"quality_metrics": [],
"reference_files": [
"/reference-files/IGVFFI8311QXYM/",
"/reference-files/IGVFFI3944QOJF/"
],
"release_timestamp": "2025-03-07T06:05:22.548936+00:00",
"s3_uri": "s3://igvf-files/2025/01/28/ab723d30-1789-49c8-a4af-ae0a05b06921/IGVFFI8511XOAV.h5",
"schema_version": "7",
"secondary_dimensions": [
"gene"
],
"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/igvf17/e17l4_raw_feature_bc_matrix.h5",
"summary": "cell by gene in raw feature barcode matrix",
"upload_status": "validated",
"uuid": "ab723d30-1789-49c8-a4af-ae0a05b06921",
"workflow": {
"@id": "/workflows/IGVFWF1453HVEC/",
"name": "Satpathy Cell Ranger",
"uniform_pipeline": false
}
}