{
"@context": "/terms/",
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"MeasurementSet",
"FileSet",
"Item"
],
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"buenrostro-bernstein:surya-mouse-colon_mm-set34"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002631/",
"assay_slims": [
"gene expression"
],
"status": "released",
"term_name": "single-cell RNA sequencing assay"
},
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{
"category": "missing publication",
"detail": "Measurement set [IGVFDS0262EFJS](/measurement-sets/IGVFDS0262EFJS/) 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/IGVFDS0262EFJS/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0262EFJS](/measurement-sets/IGVFDS0262EFJS/) has in progress subobject tabular file [IGVFFI9683HRGJ](/tabular-files/IGVFFI9683HRGJ/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0262EFJS/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0262EFJS](/measurement-sets/IGVFDS0262EFJS/) has in progress subobject tabular file [IGVFFI4393VVCW](/tabular-files/IGVFFI4393VVCW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0262EFJS/"
},
{
"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/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS0262EFJS](/measurement-sets/IGVFDS0262EFJS/) 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/IGVFDS0262EFJS/"
}
]
},
"award": {
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"component": "mapping",
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"title": "Jason Buenrostro"
},
"title": "A foundational resource of functional elements, TF footprints and gene regulatory interactions"
},
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"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/IGVFDO4618QNAL/",
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],
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"status": "released",
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},
{
"@id": "/rodent-donors/IGVFDO6240POWU/",
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],
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},
{
"@id": "/rodent-donors/IGVFDO4498WUFA/",
"accession": "IGVFDO4498WUFA",
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],
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"status": "released",
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},
{
"@id": "/rodent-donors/IGVFDO5516DGOZ/",
"accession": "IGVFDO5516DGOZ",
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],
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"status": "released",
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},
{
"@id": "/rodent-donors/IGVFDO6069WQXD/",
"accession": "IGVFDO6069WQXD",
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"buenrostro-bernstein:surya-DSS21BC-DSS-m3"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO4379PNRX/",
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],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
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{
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"accession": "IGVFFI4885KWUD",
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],
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"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
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"upload_status": "validated"
},
{
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],
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"controlled_access": false,
"creation_timestamp": "2025-02-07T18:04:43.950506+00:00",
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"href": "/sequence-files/IGVFFI8469AYWW/@@download/IGVFFI8469AYWW.fastq.gz",
"s3_uri": "s3://igvf-files/2025/02/07/c296d1d6-0e28-4884-b32f-7a9be918c939/IGVFFI8469AYWW.fastq.gz",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3782CFTC/",
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],
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"creation_timestamp": "2025-03-18T17:54:13.474092+00:00",
"file_format": "yaml",
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"href": "/configuration-files/IGVFFI3782CFTC/@@download/IGVFFI3782CFTC.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/18/732d4eea-0b83-4438-bc91-cc29017bc0f0/IGVFFI3782CFTC.yaml.gz",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9358RLQV/",
"accession": "IGVFFI9358RLQV",
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"buenrostro-bernstein:surya-DSS21BC-8k-RNA.barcode.fastq.gz"
],
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"creation_timestamp": "2025-03-14T15:49:24.590630+00:00",
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"s3_uri": "s3://igvf-files/2025/03/14/2a12cbc8-5757-4fc5-88e9-3be18291617e/IGVFFI9358RLQV.fastq.gz",
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}
],
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],
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"title": "Jason Buenrostro, Broad"
},
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"onlist_files": [
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"/tabular-files/IGVFFI9683HRGJ/"
],
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"protocols": [
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],
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{
"@id": "/measurement-sets/IGVFDS9059ORGF/",
"accession": "IGVFDS9059ORGF",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS3674UEBD/",
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},
{
"@id": "/measurement-sets/IGVFDS2183INAQ/",
"accession": "IGVFDS2183INAQ",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS3954OIWN/",
"accession": "IGVFDS3954OIWN",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6770YNZR/",
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"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS0255ZBJH/",
"accession": "IGVFDS0255ZBJH",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS7053XLPM/",
"accession": "IGVFDS7053XLPM",
"status": "released"
}
],
"release_timestamp": "2025-03-26T17:33:57.813572+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": [
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],
"institutional_certificates": [],
"sample_terms": [
{
"@id": "/sample-terms/UBERON_0000397/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
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"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"
}
],
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"status": "released",
"submitted_by": {
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"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-02-07T18:04:43.950506+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "df5b4066-226a-432f-b868-56233d81ec7e"
}