{
"@context": "/terms/",
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"@type": [
"TabularFile",
"File",
"Item"
],
"accession": "IGVFFI1739UIIK",
"aliases": [
"ansuman-satpathy:igvf17_fragments_10x5"
],
"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"
},
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"checkfiles_version": "v14",
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"content_type": "fragments",
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"creation_timestamp": "2025-01-28T06:34:22.132552+00:00",
"derived_from": [
"/sequence-files/IGVFFI2596LSMK/",
"/sequence-files/IGVFFI9012KXMP/",
"/sequence-files/IGVFFI8038EJCJ/",
"/sequence-files/IGVFFI3411XPKJ/",
"/sequence-files/IGVFFI0684TZKU/",
"/sequence-files/IGVFFI9145WIEG/",
"/sequence-files/IGVFFI9609FIPP/",
"/sequence-files/IGVFFI8106XTBI/",
"/sequence-files/IGVFFI2009YGMF/",
"/sequence-files/IGVFFI6326NWRY/",
"/sequence-files/IGVFFI9935KDDP/",
"/sequence-files/IGVFFI5318ECFS/",
"/sequence-files/IGVFFI4289YRWW/",
"/sequence-files/IGVFFI9899OUBP/",
"/sequence-files/IGVFFI7711NKNU/",
"/sequence-files/IGVFFI2929ACRM/"
],
"file_format": "tsv",
"file_format_specifications": [
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],
"file_set": {
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"accession": "IGVFDS0398ALPE",
"file_set_type": "intermediate analysis",
"samples": [
{
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"classifications": [
"differentiated cell specimen",
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],
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"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/",
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],
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{
"@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/",
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"differentiated cell specimen",
"multiplexed sample"
],
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{
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"status": "released",
"term_name": "RUES2"
}
],
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"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": []
},
{
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"differentiated cell specimen",
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],
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{
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"status": "released",
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}
],
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"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": []
},
{
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"differentiated cell specimen",
"multiplexed sample"
],
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{
"@id": "/sample-terms/EFO_0009320/",
"status": "released",
"term_name": "RUES2"
}
],
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"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"
},
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"gene_list_for": [],
"href": "/tabular-files/IGVFFI1739UIIK/@@download/IGVFFI1739UIIK.tsv.gz",
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],
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"lab": {
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"title": "Ansuman Satpathy, Stanford"
},
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"md5sum": "536bbcfe7f31cdd239bda5c5bb48e764",
"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": "2025-03-07T06:05:30.964029+00:00",
"s3_uri": "s3://igvf-files/2025/01/28/d1dea095-9d31-443d-a858-3bbee7fbe996/IGVFFI1739UIIK.tsv.gz",
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"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/e17l5_fragments.tsv.gz",
"summary": "fragments",
"upload_status": "validation exempted",
"uuid": "d1dea095-9d31-443d-a858-3bbee7fbe996",
"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
}
}