{
"@context": "/terms/",
"@id": "/analysis-sets/IGVFDS5153IDEO/",
"@type": [
"AnalysisSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5153IDEO",
"aliases": [
"buenrostro-bernstein:surya-mouse-colitis-tissue-analysis-set"
],
"assay_titles": [
"SHARE-seq"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Tissue [IGVFSM6844DNNZ](/tissues/IGVFSM6844DNNZ/) 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": "/tissues/IGVFSM6844DNNZ/"
},
{
"category": "missing publication",
"detail": "Analysis set [IGVFDS5153IDEO](/analysis-sets/IGVFDS5153IDEO/) 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/IGVFDS5153IDEO/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI1253YWWF](/matrix-files/IGVFFI1253YWWF/) has in progress subobject reference file [IGVFFI4319MSMI](/reference-files/IGVFFI4319MSMI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI1253YWWF/"
},
{
"category": "mismatched status",
"detail": "Released matrix file [IGVFFI1253YWWF](/matrix-files/IGVFFI1253YWWF/) has in progress subobject reference file [IGVFFI6909ZBPJ](/reference-files/IGVFFI6909ZBPJ/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/matrix-files/IGVFFI1253YWWF/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM6844DNNZ](/tissues/IGVFSM6844DNNZ/) is missing `upper_bound_age`, `lower_bound_age`, and `age_units`. Tissues, primary cells, and whole organisms are expected to specify a lower bound age, upper bound age, and age units.",
"level": 40,
"level_name": "WARNING",
"name": "audit_biosample_age",
"path": "/tissues/IGVFSM6844DNNZ/"
}
]
},
"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": "2025-03-06T16:19:39.191296+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO8555YQES/",
"accession": "IGVFDO8555YQES",
"aliases": [
"buenrostro-bernstein:surya-APC01-A1-13B"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO7909DHIA/",
"accession": "IGVFDO7909DHIA",
"aliases": [
"buenrostro-bernstein:surya-APC01-A1-11B"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO0418WVMT/",
"accession": "IGVFDO0418WVMT",
"aliases": [
"buenrostro-bernstein:surya-APC01-B1-6B"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO1366PENC/",
"accession": "IGVFDO1366PENC",
"aliases": [
"buenrostro-bernstein:surya-APC01-B1-4B"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO6621DZIL/",
"accession": "IGVFDO6621DZIL",
"aliases": [
"buenrostro-bernstein:surya-APC01-A1-7B"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
}
],
"file_set_type": "intermediate analysis",
"files": [
{
"@id": "/matrix-files/IGVFFI1253YWWF/",
"accession": "IGVFFI1253YWWF",
"aliases": [
"buenrostro-bernstein:surya-mouse-colitis-adenoma-tissue-rna-matrix"
],
"content_type": "sparse gene count matrix",
"creation_timestamp": "2025-03-06T16:38:17.085561+00:00",
"file_format": "h5ad",
"file_size": 10379994,
"href": "/matrix-files/IGVFFI1253YWWF/@@download/IGVFFI1253YWWF.h5ad",
"s3_uri": "s3://igvf-files/2025/03/06/a07c41fc-1078-4a83-b0a8-beb9b9c4ed32/IGVFFI1253YWWF.h5ad",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/surya-mouse-colitis/processed-data/mouse_adenoma_tissue.RNA.raw_counts.h5",
"upload_status": "validated"
},
{
"@id": "/tabular-files/IGVFFI5029GJRL/",
"accession": "IGVFFI5029GJRL",
"aliases": [
"buenrostro-bernstein:surya-mouse-colitis-adenoma-tissue-atac-frag"
],
"content_type": "fragments",
"controlled_access": false,
"creation_timestamp": "2025-03-06T16:38:46.983492+00:00",
"file_format": "tsv",
"file_size": 4005456529,
"href": "/tabular-files/IGVFFI5029GJRL/@@download/IGVFFI5029GJRL.tsv.gz",
"s3_uri": "s3://igvf-files/2025/03/06/5301fb30-e9f6-47f8-a714-720b67db47b9/IGVFFI5029GJRL.tsv.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/surya-mouse-colitis/processed-data/mouse_adenoma_tissue.ATAC.fragments.tsv.gz",
"upload_status": "validated"
}
],
"functional_assay_mechanisms": [],
"input_file_sets": [
{
"@id": "/measurement-sets/IGVFDS6123LRGF/",
"accession": "IGVFDS6123LRGF",
"aliases": [
"buenrostro-bernstein:surya-mouse-colon_mm-set25"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4128FOHH/",
"accession": "IGVFDS4128FOHH",
"aliases": [
"buenrostro-bernstein:surya-mouse-colon_mm-set26"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS9209XACN/",
"accession": "IGVFDS9209XACN",
"aliases": [
"buenrostro-bernstein:surya-mouse-colon_mm-set27"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS5523WWKM/",
"accession": "IGVFDS5523WWKM",
"aliases": [
"buenrostro-bernstein:surya-mouse-colon_mm-set28"
],
"file_set_type": "experimental data",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS3977RUCK/",
"accession": "IGVFDS3977RUCK",
"aliases": [
"buenrostro-bernstein:surya-mouse-colon_mm-set29"
],
"file_set_type": "experimental data",
"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": "2025-03-26T19:25:46.440541+00:00",
"sample_summary": "Mus musculus colon tissue",
"samples": [
{
"@id": "/tissues/IGVFSM6844DNNZ/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6844DNNZ",
"aliases": [
"buenrostro-bernstein:surya-APC01-A1-7B,APC01-B1-4B,APC01-A1-11B,APC01-A1-13B,APC01-B1-6B"
],
"classifications": [
"tissue"
],
"institutional_certificates": [],
"sample_terms": [
{
"@id": "/sample-terms/UBERON_0001155/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "colon",
"term_name": "colon"
}
],
"status": "released",
"summary": "Mus musculus C57BL/6J colon tissue",
"taxa": "Mus musculus"
}
],
"schema_version": "9",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-06T16:38:17.085561+00:00",
"summary": "SHARE-seq: fragments, sparse gene count matrix",
"uuid": "e13e9208-3ece-4768-8b6e-18c4b7227955",
"workflows": [
{
"@id": "/workflows/IGVFWF0507XZOR/",
"accession": "IGVFWF0507XZOR",
"name": "SHARE-seq-alignmentV2",
"status": "released",
"uniform_pipeline": false
}
]
}