{
"@context": "/terms/",
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"File",
"Item"
],
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"aliases": [
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],
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"assay_titles": [
"10x multiome with MULTI-seq"
],
"audit": {},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization"
},
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"checkfiles_version": "v14",
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"content_type": "fragments",
"controlled_access": true,
"creation_timestamp": "2025-01-28T06:17:04.357023+00:00",
"derived_from": [
"/sequence-files/IGVFFI0989FQEB/",
"/sequence-files/IGVFFI1807HQPL/",
"/sequence-files/IGVFFI7373LWNH/",
"/sequence-files/IGVFFI3258FOAH/",
"/sequence-files/IGVFFI0760ACLV/",
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"/sequence-files/IGVFFI5162HKBB/",
"/sequence-files/IGVFFI1651QMWN/",
"/sequence-files/IGVFFI3072OFFU/",
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"/sequence-files/IGVFFI0674WDNY/",
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],
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"file_set_type": "intermediate analysis",
"samples": [
{
"@id": "/multiplexed-samples/IGVFSM1640UGWP/",
"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM1640UGWP",
"classifications": [
"differentiated cell specimen",
"tissue",
"multiplexed sample"
],
"disease_terms": [],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/CL_0000236/",
"status": "released",
"term_name": "B cell"
},
{
"@id": "/sample-terms/UBERON_0002371/",
"status": "released",
"term_name": "bone marrow"
}
],
"status": "released",
"summary": "multiplexed sample: Homo sapiens (female) B differentiated cell specimen induced to plasmablast for 6 days; Homo sapiens (female) B differentiated cell specimen induced to plasmablast for 5 days; ... 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"
},
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"gene_list_for": [],
"href": "/tabular-files/IGVFFI8471WSXF/@@download/IGVFFI8471WSXF.tsv.gz",
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"lab": {
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"title": "Ansuman Satpathy, Stanford"
},
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"md5sum": "07fabac3840fecf996585e2c62ac51bb",
"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": "2025-03-22T00:43:36.910936+00:00",
"s3_uri": "s3://igvf-restricted-files/2025/01/28/b1070d0e-c2c5-4c20-a08a-44777f4e65d4/IGVFFI8471WSXF.tsv.gz",
"schema_version": "15",
"status": "released",
"submitted_by": {
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"title": "Christopher Mcginnis"
},
"submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf12/e12l5_fragments.tsv.gz",
"summary": "fragments",
"upload_status": "validation exempted",
"uuid": "b1070d0e-c2c5-4c20-a08a-44777f4e65d4",
"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": {
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"name": "Satpathy Cell Ranger",
"uniform_pipeline": false
}
}