{
"@context": "/terms/",
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"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2183INAQ",
"aliases": [
"buenrostro-bernstein:surya-mouse-colon_mm-set37"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002631/",
"assay_slims": [
"gene expression"
],
"status": "released",
"term_name": "single-cell RNA sequencing assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS2183INAQ](/measurement-sets/IGVFDS2183INAQ/) 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/IGVFDS2183INAQ/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS2183INAQ](/measurement-sets/IGVFDS2183INAQ/) has in progress subobject tabular file [IGVFFI9683HRGJ](/tabular-files/IGVFFI9683HRGJ/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS2183INAQ/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS2183INAQ](/measurement-sets/IGVFDS2183INAQ/) has in progress subobject tabular file [IGVFFI4393VVCW](/tabular-files/IGVFFI4393VVCW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS2183INAQ/"
},
{
"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 [IGVFDS2183INAQ](/measurement-sets/IGVFDS2183INAQ/) 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/IGVFDS2183INAQ/"
}
]
},
"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": "2025-02-07T18:03:52.096074+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/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/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/IGVFDO4379PNRX/",
"accession": "IGVFDO4379PNRX",
"aliases": [
"buenrostro-bernstein:surya-DSS21BC-DSS-m2"
],
"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"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
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"accession": "IGVFFI1779UNVR",
"aliases": [
"buenrostro-bernstein:surya-DSS21BC-more2-2-RNA.R1.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-07T18:04:50.401754+00:00",
"file_format": "fastq",
"file_size": 20401373205,
"href": "/sequence-files/IGVFFI1779UNVR/@@download/IGVFFI1779UNVR.fastq.gz",
"s3_uri": "s3://igvf-files/2025/02/07/8d4987a0-6298-46ac-973c-e22f4facb859/IGVFFI1779UNVR.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-more2-2-RNA.R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2979RGGQ/",
"accession": "IGVFFI2979RGGQ",
"aliases": [
"buenrostro-bernstein:surya-DSS21BC-more2-2-RNA.R2.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-07T18:05:02.541853+00:00",
"file_format": "fastq",
"file_size": 20847183453,
"href": "/sequence-files/IGVFFI2979RGGQ/@@download/IGVFFI2979RGGQ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/02/07/d622ef88-c3e8-43f2-9273-c6bb4a53d828/IGVFFI2979RGGQ.fastq.gz",
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"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
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"submitted_file_name": "gs://sw-igvf-submission/surya-mouse-colitis/submit-fqs/DSS21BC-more2-2-RNA.R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6114VBKZ/",
"accession": "IGVFFI6114VBKZ",
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"buenrostro-bernstein:IGVFFI1779UNVR_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-18T17:54:14.803406+00:00",
"file_format": "yaml",
"file_size": 1240,
"href": "/configuration-files/IGVFFI6114VBKZ/@@download/IGVFFI6114VBKZ.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/18/5067fdeb-5be0-47ef-a638-3f636f1c9c53/IGVFFI6114VBKZ.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/surya-mouse-colitis/seqspecs/IGVFFI1779UNVR_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0701QRLV/",
"accession": "IGVFFI0701QRLV",
"aliases": [
"buenrostro-bernstein:surya-DSS21BC-more2-2-RNA.barcode.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-14T15:49:30.880549+00:00",
"file_format": "fastq",
"file_size": 8543224669,
"href": "/sequence-files/IGVFFI0701QRLV/@@download/IGVFFI0701QRLV.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/14/9ee6678b-25d9-471e-b4eb-cef066395df6/IGVFFI0701QRLV.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
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"submitted_file_name": "gs://sw-igvf-submission/surya-mouse-colitis/submit-fqs/barcode-file/DSS21BC-more2-2-RNA.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/IGVFDS3954OIWN/",
"accession": "IGVFDS3954OIWN",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS0262EFJS/",
"accession": "IGVFDS0262EFJS",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6770YNZR/",
"accession": "IGVFDS6770YNZR",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS0255ZBJH/",
"accession": "IGVFDS0255ZBJH",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS7053XLPM/",
"accession": "IGVFDS7053XLPM",
"status": "released"
}
],
"release_timestamp": "2025-03-26T17:33:59.338794+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": "2025-02-07T18:04:50.401754+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "97d84812-a45a-4aa0-9ec6-4f38c7c38a4b"
}