{
"@context": "/terms/",
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"FileSet",
"Item"
],
"accession": "IGVFDS0718WXPI",
"aliases": [
"buenrostro-bernstein:surya-human-invitro-analysis-set"
],
"assay_titles": [
"SHARE-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM7625PGWV](/in-vitro-systems/IGVFSM7625PGWV/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM7625PGWV/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM7625PGWV](/in-vitro-systems/IGVFSM7625PGWV/) 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/IGVFSM7625PGWV/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS0718WXPI](/analysis-sets/IGVFDS0718WXPI/) 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/IGVFDS0718WXPI/"
}
]
},
"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": [],
"controlled_access": true,
"creation_timestamp": "2025-03-06T16:47:52.680990+00:00",
"data_use_limitation_summaries": [
"HMB-MDS"
],
"donors": [
{
"@id": "/human-donors/IGVFDO8630TWDU/",
"accession": "IGVFDO8630TWDU",
"aliases": [
"buenrostro-bernstein:surya-H371 57_to_72"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO7463WRZR/",
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],
"sex": "unspecified",
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"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO9637UZMV/",
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"aliases": [
"buenrostro-bernstein:surya-H492A 89_to_96"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO3401QPKA/",
"accession": "IGVFDO3401QPKA",
"aliases": [
"buenrostro-bernstein:surya-H456 17_to_32"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO1048RJRX/",
"accession": "IGVFDO1048RJRX",
"aliases": [
"buenrostro-bernstein:surya-H443 1_to_16"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
},
{
"@id": "/human-donors/IGVFDO5812FFJI/",
"accession": "IGVFDO5812FFJI",
"aliases": [
"buenrostro-bernstein:surya-H514 73_to_88"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/matrix-files/IGVFFI8142SBEI/",
"accession": "IGVFFI8142SBEI",
"aliases": [
"buenrostro-bernstein:surya-human-organoid-rna-matrix"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-03-06T16:51:56.240180+00:00",
"file_format": "h5ad",
"file_size": 63881699,
"href": "/matrix-files/IGVFFI8142SBEI/@@download/IGVFFI8142SBEI.h5ad",
"s3_uri": "s3://igvf-files/2025/03/06/3a7b359e-39f7-4240-a6ee-703e6299455b/IGVFFI8142SBEI.h5ad",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/surya-mouse-colitis/processed-data/human_organoids.RNA.raw_counts.h5",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI9764GKVR/",
"accession": "IGVFFI9764GKVR",
"aliases": [
"buenrostro-bernstein:surya-human-organoid-atac-frag"
],
"content_type": "fragments",
"controlled_access": false,
"creation_timestamp": "2025-03-06T16:56:56.030217+00:00",
"file_format": "tsv",
"file_size": 1206512769,
"href": "/tabular-files/IGVFFI9764GKVR/@@download/IGVFFI9764GKVR.tsv.gz",
"s3_uri": "s3://igvf-files/2025/03/06/cc1d12c6-4a61-401c-bbb8-21314b1d6cd0/IGVFFI9764GKVR.tsv.gz",
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"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS2259DWKL/",
"accession": "IGVFDS2259DWKL",
"aliases": [
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],
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"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS2534CJYA/",
"accession": "IGVFDS2534CJYA",
"aliases": [
"buenrostro-bernstein:surya-human-organoids_mm-set39"
],
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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": "2025-03-26T19:25:47.917944+00:00",
"sample_summary": "Homo sapiens colon epithelial cell organoid induced to colon, at 7 day(s) post change",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7625PGWV/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7625PGWV",
"aliases": [
"buenrostro-bernstein:surya-H443 1_to_16, H456 17_to_32, H462 33_to_48, H511 49_to_56, H371 57_to_72, H514 73_to_88, H492A 89_to_96"
],
"classifications": [
"organoid"
],
"institutional_certificates": [
{
"@id": "/institutional-certificates/49b4e1cd-3aa4-454f-b58f-34a0d79fefee/",
"certificate_identifier": "IP113-28",
"controlled_access": true,
"data_use_limitation": "HMB",
"data_use_limitation_modifiers": [
"MDS"
],
"status": "in progress"
},
{
"@id": "/institutional-certificates/c3a24445-2283-427d-a290-65a31b86ffd0/",
"certificate_identifier": "IP113-29",
"controlled_access": true,
"data_use_limitation": "HMB",
"data_use_limitation_modifiers": [
"MDS"
],
"status": "in progress"
}
],
"sample_terms": [
{
"@id": "/sample-terms/CL_0011108/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "colon epithelial cell",
"term_name": "colon epithelial cell"
}
],
"status": "released",
"summary": "Homo sapiens colon epithelial cell organoid induced to colon for 7 days",
"targeted_sample_term": {
"@id": "/sample-terms/UBERON_0001155/",
"status": "released",
"term_name": "colon"
},
"taxa": "Homo sapiens"
}
],
"schema_version": "9",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-06T16:51:56.240180+00:00",
"summary": "SHARE-seq: fragments, sparse gene count matrix",
"uuid": "c5b76620-4de0-4592-84a6-84bc0b4e0d31",
"workflows": [
{
"@id": "/workflows/IGVFWF0507XZOR/",
"accession": "IGVFWF0507XZOR",
"name": "SHARE-seq-alignmentV2",
"status": "released",
"uniform_pipeline": false
}
]
}