{
"@context": "/terms/",
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"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8556WPGM",
"aliases": [
"bradley-bernstein:scATAC Lib 114",
"buenrostro-bernstein:scATAC Lib 114"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002764/",
"assay_slims": [
"chromatin accessibility"
],
"status": "released",
"term_name": "single-cell ATAC-seq"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS8556WPGM](/measurement-sets/IGVFDS8556WPGM/) has in progress subobject tabular file [IGVFFI0400MBIM](/tabular-files/IGVFFI0400MBIM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS8556WPGM/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM8719IQYM](/tissues/IGVFSM8719IQYM/) 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/IGVFSM8719IQYM/"
}
]
},
"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": "2023-08-28T17:58:18.008140+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO1318PLKS/",
"accession": "IGVFDO1318PLKS",
"aliases": [
"bradley-bernstein:Donor 1503",
"buenrostro-bernstein:Donor 1503"
],
"sex": "female",
"status": "released",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
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"accession": "IGVFFI1001KYTA",
"aliases": [
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"bradley-bernstein:SS-LS_238_R1",
"buenrostro-bernstein:SS-LS_2034_R1",
"buenrostro-bernstein:SS-LS_238_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T18:21:02.712079+00:00",
"file_format": "fastq",
"file_size": 635359937,
"href": "/sequence-files/IGVFFI1001KYTA/@@download/IGVFFI1001KYTA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/08/28/1f44bfd8-a49a-4da2-a542-51739fd95e93/IGVFFI1001KYTA.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-159_L2_SS-PKR-130_2022-APRIL-R1-PLATE2-ENTIRE-PLATE_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2975AWSJ/",
"accession": "IGVFFI2975AWSJ",
"aliases": [
"bradley-bernstein:SS-LS_2006_R1",
"bradley-bernstein:SS-LS_38_R1",
"buenrostro-bernstein:SS-LS_2006_R1",
"buenrostro-bernstein:SS-LS_38_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T18:20:58.761563+00:00",
"file_format": "fastq",
"file_size": 632951602,
"href": "/sequence-files/IGVFFI2975AWSJ/@@download/IGVFFI2975AWSJ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/08/28/3be3b9e3-e79a-4881-bf3e-027483cb9234/IGVFFI2975AWSJ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-159_L1_SS-PKR-130_2022-APRIL-R1-PLATE2-ENTIRE-PLATE_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4364SHWE/",
"accession": "IGVFFI4364SHWE",
"aliases": [
"bradley-bernstein:SS-LS_2034_R2",
"bradley-bernstein:SS-LS_238_R2",
"buenrostro-bernstein:SS-LS_2034_R2",
"buenrostro-bernstein:SS-LS_238_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T18:21:03.574708+00:00",
"file_format": "fastq",
"file_size": 1140871757,
"href": "/sequence-files/IGVFFI4364SHWE/@@download/IGVFFI4364SHWE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/08/28/85597775-e76e-42b1-99d9-456774d35c29/IGVFFI4364SHWE.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-159_L2_SS-PKR-130_2022-APRIL-R1-PLATE2-ENTIRE-PLATE_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6665GUBQ/",
"accession": "IGVFFI6665GUBQ",
"aliases": [
"bradley-bernstein:SS-LS_2006_R2",
"bradley-bernstein:SS-LS_38_R2",
"buenrostro-bernstein:SS-LS_2006_R2",
"buenrostro-bernstein:SS-LS_38_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T18:20:59.795074+00:00",
"file_format": "fastq",
"file_size": 1136249944,
"href": "/sequence-files/IGVFFI6665GUBQ/@@download/IGVFFI6665GUBQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/08/28/ff4d0a70-32c0-41bc-9cf7-35823dffc226/IGVFFI6665GUBQ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-159_L1_SS-PKR-130_2022-APRIL-R1-PLATE2-ENTIRE-PLATE_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5892NIPL/",
"accession": "IGVFFI5892NIPL",
"aliases": [
"bradley-bernstein:SS-LS_2006_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:49:54.723149+00:00",
"file_format": "yaml",
"file_size": 1188,
"href": "/configuration-files/IGVFFI5892NIPL/@@download/IGVFFI5892NIPL.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/17/445d714c-df51-4594-8ebd-022db0533d69/IGVFFI5892NIPL.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_2006_seqspecv3.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2356MCSL/",
"accession": "IGVFFI2356MCSL",
"aliases": [
"bradley-bernstein:SS-LS_2034_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:49:48.123344+00:00",
"file_format": "yaml",
"file_size": 1188,
"href": "/configuration-files/IGVFFI2356MCSL/@@download/IGVFFI2356MCSL.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/17/1d5243e8-a26c-4608-9c80-697fe8780bbb/IGVFFI2356MCSL.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_2034_seqspecv3.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS0635KHHW/"
],
"lab": {
"@id": "/labs/jason-buenrostro/",
"title": "Jason Buenrostro, Broad"
},
"multiome_size": 6,
"notes": "Preferred_assay_titles enum SHARE-Seq has been renamed to be SHARE-seq.",
"onlist_files": [
"/tabular-files/IGVFFI0400MBIM/"
],
"onlist_method": "product",
"preferred_assay_title": "SHARE-seq",
"protocols": [
"https://www.protocols.io/view/share-seq-protocol-v2-2-di3y4gpw"
],
"related_multiome_datasets": [
{
"@id": "/measurement-sets/IGVFDS3032KHHX/",
"accession": "IGVFDS3032KHHX",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS9693BTRP/",
"accession": "IGVFDS9693BTRP",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS0877CWMW/",
"accession": "IGVFDS0877CWMW",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4704VICJ/",
"accession": "IGVFDS4704VICJ",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6361NSJR/",
"accession": "IGVFDS6361NSJR",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:18:34.447848+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM8719IQYM/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8719IQYM",
"aliases": [
"bradley-bernstein:BioSam 4561_SS-PKR 130",
"buenrostro-bernstein:BioSam 4561_SS-PKR 130"
],
"cellular_sub_pool": "SS-PKR 130",
"classifications": [
"tissue"
],
"institutional_certificates": [],
"sample_terms": [
{
"@id": "/sample-terms/UBERON_0000955/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "brain",
"term_name": "brain"
}
],
"status": "released",
"summary": "Mus musculus C57BL/6 (female) brain tissue (cellular sub pool: SS-PKR 130)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2023-08-28T18:20:58.761563+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "b0bf269f-e7e5-431d-baf0-52c42ac67076"
}