{
"@context": "/terms/",
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"@type": [
"TabularFile",
"File",
"Item"
],
"accession": "IGVFFI0224OXYI",
"aliases": [
"ansuman-satpathy:igvf6_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": "f5b20dba659e9d5dff5b92835e4ddafd",
"content_type": "fragments",
"controlled_access": false,
"creation_timestamp": "2025-01-28T06:00:47.191584+00:00",
"derived_from": [
"/sequence-files/IGVFFI9445PPMH/",
"/sequence-files/IGVFFI1872OAKD/",
"/sequence-files/IGVFFI1806XLTF/",
"/sequence-files/IGVFFI3461DLIM/",
"/sequence-files/IGVFFI6267BAKM/",
"/sequence-files/IGVFFI8873EKRF/",
"/sequence-files/IGVFFI3484GCTZ/",
"/sequence-files/IGVFFI4396FQJJ/",
"/sequence-files/IGVFFI7182CDWE/",
"/sequence-files/IGVFFI7081YWVG/",
"/sequence-files/IGVFFI7722TXFD/",
"/sequence-files/IGVFFI2966CCDM/"
],
"file_format": "tsv",
"file_format_specifications": [
"/documents/43920105-5f77-430a-9bcd-f00180ff2b1d/"
],
"file_set": {
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"accession": "IGVFDS3232NVVG",
"file_set_type": "intermediate analysis",
"samples": [
{
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"accession": "IGVFSM8276PHGD",
"classifications": [
"cell line",
"differentiated cell specimen",
"multiplexed sample"
],
"disease_terms": [],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0003042/",
"status": "released",
"term_name": "H1-hESC"
}
],
"status": "released",
"summary": "multiplexed sample: H1-hESC differentiated cell specimen induced to islet of Langerhans for 18 days, male, Homo sapiens; H1-hESC differentiated cell specimen induced to islet of Langerhans for 7 days, male, Homo sapiens; ... and 6 more samples",
"taxa": "Homo sapiens",
"treatments": []
},
{
"@id": "/multiplexed-samples/IGVFSM2522EBPE/",
"accession": "IGVFSM2522EBPE",
"classifications": [
"cell line",
"differentiated cell specimen",
"multiplexed sample"
],
"disease_terms": [],
"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0003042/",
"status": "released",
"term_name": "H1-hESC"
}
],
"status": "released",
"summary": "multiplexed sample: H1-hESC differentiated cell specimen induced to islet of Langerhans for 18 days, male, Homo sapiens; H1-hESC differentiated cell specimen induced to islet of Langerhans for 7 days, male, Homo sapiens; ... and 6 more samples",
"taxa": "Homo sapiens",
"treatments": []
},
{
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"classifications": [
"cell line",
"differentiated cell specimen",
"multiplexed sample"
],
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"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0003042/",
"status": "released",
"term_name": "H1-hESC"
}
],
"status": "released",
"summary": "multiplexed sample: H1-hESC differentiated cell specimen induced to islet of Langerhans for 18 days, male, Homo sapiens; H1-hESC differentiated cell specimen induced to islet of Langerhans for 7 days, male, Homo sapiens; ... and 6 more samples",
"taxa": "Homo sapiens",
"treatments": []
},
{
"@id": "/multiplexed-samples/IGVFSM8961ZZQN/",
"accession": "IGVFSM8961ZZQN",
"classifications": [
"cell line",
"differentiated cell specimen",
"multiplexed sample"
],
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"modifications": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0003042/",
"status": "released",
"term_name": "H1-hESC"
}
],
"status": "released",
"summary": "multiplexed sample: H1-hESC differentiated cell specimen induced to islet of Langerhans for 18 days, male, Homo sapiens; H1-hESC differentiated cell specimen induced to islet of Langerhans for 7 days, male, Homo sapiens; ... and 6 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/IGVFFI0224OXYI/@@download/IGVFFI0224OXYI.tsv.gz",
"input_file_for": [
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"/tabular-files/IGVFFI4030SCVB/"
],
"integrated_in": [],
"lab": {
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"title": "Ansuman Satpathy, Stanford"
},
"loci_list_for": [],
"md5sum": "8ea13dfa3981d61429ff5a3568a1c95a",
"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": "2025-03-07T06:04:51.091648+00:00",
"s3_uri": "s3://igvf-files/2025/01/28/72c0d9bb-caab-4d07-bae8-c19de6e30bde/IGVFFI0224OXYI.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/igvf6/e6l4_fragments.tsv.gz",
"summary": "fragments",
"upload_status": "validation exempted",
"uuid": "72c0d9bb-caab-4d07-bae8-c19de6e30bde",
"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
}
}