{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6770YNZR/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6770YNZR",
"aliases": [
"buenrostro-bernstein:surya-mouse-colon_mm-set32"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002764/",
"assay_slims": [
"chromatin accessibility"
],
"status": "released",
"term_name": "single-cell ATAC-seq"
},
"audit": {
"INTERNAL_ACTION": [
{
"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": "missing publication",
"detail": "Measurement set [IGVFDS6770YNZR](/measurement-sets/IGVFDS6770YNZR/) 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": "/measurement-sets/IGVFDS6770YNZR/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS6770YNZR](/measurement-sets/IGVFDS6770YNZR/) has in progress subobject tabular file [IGVFFI4393VVCW](/tabular-files/IGVFFI4393VVCW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS6770YNZR/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS6770YNZR](/measurement-sets/IGVFDS6770YNZR/) has in progress subobject tabular file [IGVFFI9683HRGJ](/tabular-files/IGVFFI9683HRGJ/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS6770YNZR/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS6770YNZR](/measurement-sets/IGVFDS6770YNZR/) is missing required `strand_specificity`. Single-cell assays are expected to specify strand specificity.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_strand_specificity",
"path": "/measurement-sets/IGVFDS6770YNZR/"
}
]
},
"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": "2025-02-07T18:03:46.357831+00:00",
"description": "Colitis_derived DSS21BC-DSS-m1,DSS21BC-DSS-m2,DSS21BC-DSS-m3; Control DSS21BC-DSS-m7,DSS21BC-DSS-m8,DSS21BC-DSS-m9",
"donors": [
{
"@id": "/rodent-donors/IGVFDO6069WQXD/",
"accession": "IGVFDO6069WQXD",
"aliases": [
"buenrostro-bernstein:surya-DSS21BC-DSS-m3"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO4498WUFA/",
"accession": "IGVFDO4498WUFA",
"aliases": [
"buenrostro-bernstein:surya-DSS21BC-DSS-m7"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO6240POWU/",
"accession": "IGVFDO6240POWU",
"aliases": [
"buenrostro-bernstein:surya-DSS21BC-DSS-m9"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO5516DGOZ/",
"accession": "IGVFDO5516DGOZ",
"aliases": [
"buenrostro-bernstein:surya-DSS21BC-DSS-m1"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO4618QNAL/",
"accession": "IGVFDO4618QNAL",
"aliases": [
"buenrostro-bernstein:surya-DSS21BC-DSS-m8"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO4379PNRX/",
"accession": "IGVFDO4379PNRX",
"aliases": [
"buenrostro-bernstein:surya-DSS21BC-DSS-m2"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/configuration-files/IGVFFI6628JTXO/",
"accession": "IGVFFI6628JTXO",
"aliases": [
"buenrostro-bernstein:IGVFFI2165FXVU_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-18T17:53:45.129661+00:00",
"file_format": "yaml",
"file_size": 1222,
"href": "/configuration-files/IGVFFI6628JTXO/@@download/IGVFFI6628JTXO.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/18/4ed580c5-1359-4c43-b69a-feb3be3fd558/IGVFFI6628JTXO.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/surya-mouse-colitis/seqspecs/IGVFFI2165FXVU_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2165FXVU/",
"accession": "IGVFFI2165FXVU",
"aliases": [
"buenrostro-bernstein:surya-DSS21BC-more2-1-ATAC.R1.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-07T18:04:40.467119+00:00",
"file_format": "fastq",
"file_size": 4286433457,
"href": "/sequence-files/IGVFFI2165FXVU/@@download/IGVFFI2165FXVU.fastq.gz",
"s3_uri": "s3://igvf-files/2025/02/07/9a475753-c287-4b6a-b6c7-61c439e0ae09/IGVFFI2165FXVU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/surya-mouse-colitis/submit-fqs/DSS21BC-more2-1-ATAC.R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8910YNPE/",
"accession": "IGVFFI8910YNPE",
"aliases": [
"buenrostro-bernstein:surya-DSS21BC-more2-1-ATAC.R2.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-07T18:04:54.910902+00:00",
"file_format": "fastq",
"file_size": 3978126555,
"href": "/sequence-files/IGVFFI8910YNPE/@@download/IGVFFI8910YNPE.fastq.gz",
"s3_uri": "s3://igvf-files/2025/02/07/eca49e56-f520-4b7b-aa7a-1c8aca56bc41/IGVFFI8910YNPE.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/surya-mouse-colitis/submit-fqs/DSS21BC-more2-1-ATAC.R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9885LMTH/",
"accession": "IGVFFI9885LMTH",
"aliases": [
"buenrostro-bernstein:surya-DSS21BC-more2-1-ATAC.barcode.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-14T15:49:20.244911+00:00",
"file_format": "fastq",
"file_size": 1635584248,
"href": "/sequence-files/IGVFFI9885LMTH/@@download/IGVFFI9885LMTH.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/14/a4ccf7d8-835e-49ba-9788-464ccad253d0/IGVFFI9885LMTH.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/surya-mouse-colitis/submit-fqs/barcode-file/DSS21BC-more2-1-ATAC.barcode.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5536ZQMO/"
],
"lab": {
"@id": "/labs/jason-buenrostro/",
"title": "Jason Buenrostro, Broad"
},
"multiome_size": 8,
"onlist_files": [
"/tabular-files/IGVFFI4393VVCW/",
"/tabular-files/IGVFFI9683HRGJ/"
],
"onlist_method": "product",
"preferred_assay_title": "SHARE-seq",
"protocols": [
"https://www.protocols.io/view/share-seq-v1-6qpvrdexpgmk/v1"
],
"related_multiome_datasets": [
{
"@id": "/measurement-sets/IGVFDS9059ORGF/",
"accession": "IGVFDS9059ORGF",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS3674UEBD/",
"accession": "IGVFDS3674UEBD",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS2183INAQ/",
"accession": "IGVFDS2183INAQ",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS3954OIWN/",
"accession": "IGVFDS3954OIWN",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS0262EFJS/",
"accession": "IGVFDS0262EFJS",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS0255ZBJH/",
"accession": "IGVFDS0255ZBJH",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS7053XLPM/",
"accession": "IGVFDS7053XLPM",
"status": "released"
}
],
"release_timestamp": "2025-03-26T17:33:48.606572+00:00",
"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"
],
"status": "released",
"summary": "colonic epithelium",
"term_name": "colonic epithelium"
}
],
"status": "released",
"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"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-02-07T18:04:40.467119+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "24f7645c-2525-4c35-9d5f-e05aefa849fe"
}