{
"@context": "/terms/",
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"AnalysisSet",
"FileSet",
"Item"
],
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],
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"SHARE-seq"
],
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"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS5536ZQMO](/analysis-sets/IGVFDS5536ZQMO/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_file_set_missing_publication",
"path": "/analysis-sets/IGVFDS5536ZQMO/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM4239FRER](/in-vitro-systems/IGVFSM4239FRER/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_sample_missing_publication",
"path": "/in-vitro-systems/IGVFSM4239FRER/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI0315UORM](/matrix-files/IGVFFI0315UORM/) has in progress subobject reference file [IGVFFI4319MSMI](/reference-files/IGVFFI4319MSMI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI0315UORM/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI0315UORM](/matrix-files/IGVFFI0315UORM/) has in progress subobject reference file [IGVFFI6909ZBPJ](/reference-files/IGVFFI6909ZBPJ/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI0315UORM/"
}
]
},
"award": {
"@id": "/awards/HG011986/",
"component": "mapping",
"contact_pi": {
"@id": "/users/33c6eb70-e143-4f77-9661-4b3905737daa/",
"title": "Jason Buenrostro"
},
"title": "A foundational resource of functional elements, TF footprints and gene regulatory interactions"
},
"control_for": [],
"creation_timestamp": "2025-03-06T16:19:40.866306+00:00",
"donors": [
{
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],
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},
{
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},
{
"@id": "/rodent-donors/IGVFDO6240POWU/",
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"buenrostro-bernstein:surya-DSS21BC-DSS-m9"
],
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},
{
"@id": "/rodent-donors/IGVFDO4498WUFA/",
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],
"sex": "unspecified",
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},
{
"@id": "/rodent-donors/IGVFDO4379PNRX/",
"accession": "IGVFDO4379PNRX",
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],
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"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO6069WQXD/",
"accession": "IGVFDO6069WQXD",
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"buenrostro-bernstein:surya-DSS21BC-DSS-m3"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
}
],
"file_set_type": "intermediate analysis",
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{
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"accession": "IGVFFI0315UORM",
"aliases": [
"buenrostro-bernstein:surya-mouse-colitis-organoid-rna-matrix"
],
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"creation_timestamp": "2025-03-06T16:38:18.620373+00:00",
"file_format": "h5ad",
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"href": "/matrix-files/IGVFFI0315UORM/@@download/IGVFFI0315UORM.h5ad",
"s3_uri": "s3://igvf-files/2025/03/06/e170e021-c397-4b37-8b4d-887a0af04eff/IGVFFI0315UORM.h5ad",
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI1146PULR/",
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"aliases": [
"buenrostro-bernstein:surya-mouse-colitis-organoid-atac-frag"
],
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"controlled_access": false,
"creation_timestamp": "2025-03-06T16:38:48.968772+00:00",
"file_format": "tsv",
"file_size": 2266989120,
"href": "/tabular-files/IGVFFI1146PULR/@@download/IGVFFI1146PULR.tsv.gz",
"s3_uri": "s3://igvf-files/2025/03/06/830bc92c-39be-48de-989f-7a88413ac9e8/IGVFFI1146PULR.tsv.gz",
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"upload_status": "validated"
}
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"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS9059ORGF/",
"accession": "IGVFDS9059ORGF",
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"buenrostro-bernstein:surya-mouse-colon_mm-set30"
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{
"@id": "/measurement-sets/IGVFDS3954OIWN/",
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"buenrostro-bernstein:surya-mouse-colon_mm-set31"
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{
"@id": "/measurement-sets/IGVFDS6770YNZR/",
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{
"@id": "/measurement-sets/IGVFDS3674UEBD/",
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"buenrostro-bernstein:surya-mouse-colon_mm-set33"
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{
"@id": "/measurement-sets/IGVFDS0262EFJS/",
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{
"@id": "/measurement-sets/IGVFDS0255ZBJH/",
"accession": "IGVFDS0255ZBJH",
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"buenrostro-bernstein:surya-mouse-colon_mm-set35"
],
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},
{
"@id": "/measurement-sets/IGVFDS7053XLPM/",
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"buenrostro-bernstein:surya-mouse-colon_mm-set36"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS2183INAQ/",
"accession": "IGVFDS2183INAQ",
"aliases": [
"buenrostro-bernstein:surya-mouse-colon_mm-set37"
],
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"status": "released"
}
],
"input_for": [],
"lab": {
"@id": "/labs/jason-buenrostro/",
"title": "Jason Buenrostro, Broad"
},
"protocols": [
"https://www.protocols.io/view/share-seq-v1-6qpvrdexpgmk/v1"
],
"release_timestamp": "2025-03-26T19:25:49.206283+00:00",
"sample_summary": "Mus musculus colonic epithelium organoid induced to colon, at 27 day(s) post change",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4239FRER/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4239FRER",
"aliases": [
"buenrostro-bernstein:surya-DSS21BC-DSS-m1,DSS21BC-DSS-m2,DSS21BC-DSS-m3,DSS21BC-DSS-m7,DSS21BC-DSS-m8,DSS21BC-DSS-m9"
],
"classifications": [
"organoid"
],
"institutional_certificates": [],
"sample_terms": [
{
"@id": "/sample-terms/UBERON_0000397/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
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"summary": "colonic epithelium",
"term_name": "colonic epithelium"
}
],
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"summary": "Mus musculus C57BL/6J colonic epithelium organoid induced to colon for 27 days",
"targeted_sample_term": {
"@id": "/sample-terms/UBERON_0001155/",
"status": "released",
"term_name": "colon"
},
"taxa": "Mus musculus"
}
],
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"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-06T16:38:18.620373+00:00",
"summary": "SHARE-seq: fragments, sparse gene count matrix",
"uuid": "72679647-abb4-40c4-8c32-b55c66206611",
"workflows": [
{
"@id": "/workflows/IGVFWF0507XZOR/",
"accession": "IGVFWF0507XZOR",
"name": "SHARE-seq-alignmentV2",
"status": "released",
"uniform_pipeline": false
}
]
}