{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4911ZDCJ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4911ZDCJ",
"aliases": [
"bradley-bernstein:scATAC Lib 110",
"buenrostro-bernstein:scATAC Lib 110"
],
"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 [IGVFSM3932SXVT](/tissues/IGVFSM3932SXVT/) 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/IGVFSM3932SXVT/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS4911ZDCJ](/measurement-sets/IGVFDS4911ZDCJ/) 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/IGVFDS4911ZDCJ/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS4911ZDCJ](/measurement-sets/IGVFDS4911ZDCJ/) has in progress subobject tabular file [IGVFFI0400MBIM](/tabular-files/IGVFFI0400MBIM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS4911ZDCJ/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS4911ZDCJ](/measurement-sets/IGVFDS4911ZDCJ/) 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/IGVFDS4911ZDCJ/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM3932SXVT](/tissues/IGVFSM3932SXVT/) 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/IGVFSM3932SXVT/"
}
]
},
"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": "2023-08-28T20:29:05.850250+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"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": [
{
"@id": "/sequence-files/IGVFFI6393JXIX/",
"accession": "IGVFFI6393JXIX",
"aliases": [
"bradley-bernstein:SS-LS_2002_R1",
"bradley-bernstein:SS-LS_42_R1",
"buenrostro-bernstein:SS-LS_2002_R1",
"buenrostro-bernstein:SS-LS_42_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-09-05T19:27:43.535917+00:00",
"file_format": "fastq",
"file_size": 118768756,
"href": "/sequence-files/IGVFFI6393JXIX/@@download/IGVFFI6393JXIX.fastq.gz",
"md5sum": "e052ceb456c77b65d6c8057d284f6e1d",
"s3_uri": "s3://igvf-files/2023/09/05/672806e7-9b5f-4048-b141-a1286ec42906/IGVFFI6393JXIX.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-155_L1_SS-PKR-129_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9528JABE/",
"accession": "IGVFFI9528JABE",
"aliases": [
"bradley-bernstein:SS-LS_2002_R2",
"bradley-bernstein:SS-LS_42_R2",
"buenrostro-bernstein:SS-LS_2002_R2",
"buenrostro-bernstein:SS-LS_42_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-09-05T19:27:44.528770+00:00",
"file_format": "fastq",
"file_size": 210057233,
"href": "/sequence-files/IGVFFI9528JABE/@@download/IGVFFI9528JABE.fastq.gz",
"md5sum": "48f32136c66f96e09cee9834a19d0ee9",
"s3_uri": "s3://igvf-files/2023/09/05/c72141b2-6554-4376-a122-cd6bf60cc545/IGVFFI9528JABE.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-155_L1_SS-PKR-129_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6331OWCQ/",
"accession": "IGVFFI6331OWCQ",
"aliases": [
"bradley-bernstein:SS-LS_2030_R1",
"bradley-bernstein:SS-LS_242_R1",
"buenrostro-bernstein:SS-LS_2030_R1",
"buenrostro-bernstein:SS-LS_242_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-09-05T19:27:54.764546+00:00",
"file_format": "fastq",
"file_size": 118568799,
"href": "/sequence-files/IGVFFI6331OWCQ/@@download/IGVFFI6331OWCQ.fastq.gz",
"md5sum": "5e2e7a606e7739c8cc3ca52c95cdb262",
"s3_uri": "s3://igvf-files/2023/09/05/72d2d631-3668-458d-bc30-3defd4d8cda8/IGVFFI6331OWCQ.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-155_L2_SS-PKR-129_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5954LBNR/",
"accession": "IGVFFI5954LBNR",
"aliases": [
"bradley-bernstein:SS-LS_2030_R2",
"bradley-bernstein:SS-LS_242_R2",
"buenrostro-bernstein:SS-LS_2030_R2",
"buenrostro-bernstein:SS-LS_242_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-09-05T19:27:55.642073+00:00",
"file_format": "fastq",
"file_size": 209800431,
"href": "/sequence-files/IGVFFI5954LBNR/@@download/IGVFFI5954LBNR.fastq.gz",
"md5sum": "43ba1db2f887c53b6fe54294df101ceb",
"s3_uri": "s3://igvf-files/2023/09/05/f35af027-d884-40f3-b84e-b94bffa6eecf/IGVFFI5954LBNR.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-155_L2_SS-PKR-129_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2269ULRS/",
"accession": "IGVFFI2269ULRS",
"aliases": [
"bradley-bernstein:SS-LS_2002_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:49:59.303007+00:00",
"file_format": "yaml",
"file_size": 1189,
"href": "/configuration-files/IGVFFI2269ULRS/@@download/IGVFFI2269ULRS.yaml.gz",
"md5sum": "3296ad04a1853500c44bb051a169031e",
"s3_uri": "s3://igvf-files/2024/09/17/e6ace8af-c6e1-4ba0-b19d-786b9ddc2ec4/IGVFFI2269ULRS.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_2002_seqspecv3.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5596YAOZ/",
"accession": "IGVFFI5596YAOZ",
"aliases": [
"bradley-bernstein:SS-LS_2030_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:49:52.702407+00:00",
"file_format": "yaml",
"file_size": 1189,
"href": "/configuration-files/IGVFFI5596YAOZ/@@download/IGVFFI5596YAOZ.yaml.gz",
"md5sum": "438f49d6ae5985046c0aa935d8af6469",
"s3_uri": "s3://igvf-files/2024/09/17/0247970f-d9a1-47c5-af95-332d811ed657/IGVFFI5596YAOZ.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_2030_seqspecv3.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS8415FVDT/"
],
"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/IGVFDS0020LQRY/",
"accession": "IGVFDS0020LQRY",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS5192VPKQ/",
"accession": "IGVFDS5192VPKQ",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8535JZRF/",
"accession": "IGVFDS8535JZRF",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS3638UVNV/",
"accession": "IGVFDS3638UVNV",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8078FJZR/",
"accession": "IGVFDS8078FJZR",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:22:39.420961+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM3932SXVT/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3932SXVT",
"aliases": [
"bradley-bernstein:BioSam 4561_SS-PKR 129",
"buenrostro-bernstein:BioSam 4561_SS-PKR 129"
],
"cellular_sub_pool": "SS-PKR 129",
"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 129)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2023-09-05T19:27:43.535917+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "118edbdf-868d-41b6-96b0-921ad6380e9e"
}