{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1554OVKW/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1554OVKW",
"aliases": [
"buenrostro-bernstein:scATAC Lib 1776"
],
"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": "Tissue [IGVFSM9407UDAJ](/tissues/IGVFSM9407UDAJ/) 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/IGVFSM9407UDAJ/"
},
{
"category": "NTR term ID",
"detail": "Sample term for [NTR_0000646](/sample-terms/NTR_0000646/) has been newly requested. Ontology terms with a newly requested term ID are expected to have it updated following its addition to the appropriate ontology database.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_ntr_term_id",
"path": "/sample-terms/NTR_0000646/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS1554OVKW](/measurement-sets/IGVFDS1554OVKW/) 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/IGVFDS1554OVKW/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS1554OVKW](/measurement-sets/IGVFDS1554OVKW/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS1554OVKW/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS1554OVKW](/measurement-sets/IGVFDS1554OVKW/) has in progress subobject tabular file [IGVFFI6680XCDT](/tabular-files/IGVFFI6680XCDT/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS1554OVKW/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS1554OVKW](/measurement-sets/IGVFDS1554OVKW/) 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/IGVFDS1554OVKW/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM9407UDAJ](/tissues/IGVFSM9407UDAJ/) 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/IGVFSM9407UDAJ/"
}
]
},
"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": "2025-03-05T15:33:59.631310+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO3508PMXX/",
"accession": "IGVFDO3508PMXX",
"aliases": [
"ali-mortazavi:768_B6J_10F",
"buenrostro-bernstein:Donor 2078"
],
"sex": "female",
"status": "released",
"strain_background": "C57BL/6J (B6)",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
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"accession": "IGVFFI6083KJKR",
"aliases": [
"buenrostro-bernstein:SS-LS_8371_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:54:08.393649+00:00",
"file_format": "fastq",
"file_size": 7561365646,
"href": "/sequence-files/IGVFFI6083KJKR/@@download/IGVFFI6083KJKR.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/9c4e8c57-68da-419f-8523-16f5ca76d20a/IGVFFI6083KJKR.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2251_L4_SS-PKR-603_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3877TEIM/",
"accession": "IGVFFI3877TEIM",
"aliases": [
"buenrostro-bernstein:SS-LS_8381_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:54:27.628524+00:00",
"file_format": "fastq",
"file_size": 7522689823,
"href": "/sequence-files/IGVFFI3877TEIM/@@download/IGVFFI3877TEIM.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/59ce9747-4b0e-4d98-a309-a195db95c447/IGVFFI3877TEIM.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
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"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2251_L5_SS-PKR-603_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0939KXTG/",
"accession": "IGVFFI0939KXTG",
"aliases": [
"buenrostro-bernstein:SS-LS_8371_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:54:06.711413+00:00",
"file_format": "fastq",
"file_size": 5307491694,
"href": "/sequence-files/IGVFFI0939KXTG/@@download/IGVFFI0939KXTG.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/b57f9d15-ad0a-48df-8fd8-045530c54672/IGVFFI0939KXTG.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2251_L4_SS-PKR-603_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6943YYXC/",
"accession": "IGVFFI6943YYXC",
"aliases": [
"buenrostro-bernstein:SS-LS_8391_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:54:49.353466+00:00",
"file_format": "fastq",
"file_size": 7597615974,
"href": "/sequence-files/IGVFFI6943YYXC/@@download/IGVFFI6943YYXC.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/3953782b-9be6-46dd-9b87-220fb8166c3b/IGVFFI6943YYXC.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2251_L6_SS-PKR-603_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1913ATIN/",
"accession": "IGVFFI1913ATIN",
"aliases": [
"buenrostro-bernstein:SS-LS_8381_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:54:25.596982+00:00",
"file_format": "fastq",
"file_size": 5309234888,
"href": "/sequence-files/IGVFFI1913ATIN/@@download/IGVFFI1913ATIN.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/18babcec-ccb0-423c-9dbc-6392462cbb84/IGVFFI1913ATIN.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2251_L5_SS-PKR-603_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3368XUML/",
"accession": "IGVFFI3368XUML",
"aliases": [
"buenrostro-bernstein:SS-LS_8391_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:54:47.246329+00:00",
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"href": "/sequence-files/IGVFFI3368XUML/@@download/IGVFFI3368XUML.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/fcc04ba7-f345-46c4-ab66-ac89b7c94029/IGVFFI3368XUML.fastq.gz",
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"status": "released",
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},
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8741JSWA/",
"accession": "IGVFFI8741JSWA",
"aliases": [
"buenrostro-bernstein:SS-LS_8381_seqspec"
],
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"creation_timestamp": "2025-03-07T20:00:10.981198+00:00",
"file_format": "yaml",
"file_size": 1248,
"href": "/configuration-files/IGVFFI8741JSWA/@@download/IGVFFI8741JSWA.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/dfc5487a-ac55-4c1e-b001-d28418eba453/IGVFFI8741JSWA.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8381_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6044TRRB/",
"accession": "IGVFFI6044TRRB",
"aliases": [
"buenrostro-bernstein:SS-LS_8391_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T20:00:21.450632+00:00",
"file_format": "yaml",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4298OFDJ/",
"accession": "IGVFFI4298OFDJ",
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"buenrostro-bernstein:SS-LS_8371_seqspec"
],
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"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS7586BQJE/"
],
"lab": {
"@id": "/labs/jason-buenrostro/",
"title": "Jason Buenrostro, Broad"
},
"multiome_size": 2,
"onlist_files": [
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"/tabular-files/IGVFFI2668ZFEB/"
],
"onlist_method": "product",
"preferred_assay_title": "SHARE-seq",
"protocols": [
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],
"related_multiome_datasets": [
{
"@id": "/measurement-sets/IGVFDS0729LSNF/",
"accession": "IGVFDS0729LSNF",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:21:53.717528+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM9407UDAJ/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9407UDAJ",
"aliases": [
"buenrostro-bernstein:BioSam 5155_SS-PKR 603"
],
"cellular_sub_pool": "SS-PKR 603",
"classifications": [
"tissue"
],
"institutional_certificates": [],
"sample_terms": [
{
"@id": "/sample-terms/NTR_0000646/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "left cerebral cortex",
"term_name": "left cerebral cortex"
}
],
"status": "released",
"summary": "Mus musculus C57BL/6J (female) left cerebral cortex tissue (cellular sub pool: SS-PKR 603)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
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},
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"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "939b24aa-d9ba-4d5b-86f8-b6e5613f9399"
}