{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3638UVNV/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3638UVNV",
"aliases": [
"bradley-bernstein:scATAC Lib 109",
"buenrostro-bernstein:scATAC Lib 109"
],
"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 [IGVFDS3638UVNV](/measurement-sets/IGVFDS3638UVNV/) 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/IGVFDS3638UVNV/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS3638UVNV](/measurement-sets/IGVFDS3638UVNV/) has in progress subobject tabular file [IGVFFI0400MBIM](/tabular-files/IGVFFI0400MBIM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS3638UVNV/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS3638UVNV](/measurement-sets/IGVFDS3638UVNV/) 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/IGVFDS3638UVNV/"
}
],
"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": "2023-08-28T20:29:06.403584+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/IGVFFI5944WRFT/",
"accession": "IGVFFI5944WRFT",
"aliases": [
"bradley-bernstein:SS-LS_2001_R1",
"bradley-bernstein:SS-LS_43_R1",
"buenrostro-bernstein:SS-LS_2001_R1",
"buenrostro-bernstein:SS-LS_43_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-09-05T19:27:45.415694+00:00",
"file_format": "fastq",
"file_size": 231961083,
"href": "/sequence-files/IGVFFI5944WRFT/@@download/IGVFFI5944WRFT.fastq.gz",
"md5sum": "57b49e39109a3d613eea22bb67d1a65c",
"s3_uri": "s3://igvf-files/2023/09/05/612a9367-4a7b-4a72-aaf3-d44b1ea75138/IGVFFI5944WRFT.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-154_L1_SS-PKR-129_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9706EHIQ/",
"accession": "IGVFFI9706EHIQ",
"aliases": [
"bradley-bernstein:SS-LS_2001_R2",
"bradley-bernstein:SS-LS_43_R2",
"buenrostro-bernstein:SS-LS_2001_R2",
"buenrostro-bernstein:SS-LS_43_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-09-05T19:27:46.348853+00:00",
"file_format": "fastq",
"file_size": 412091150,
"href": "/sequence-files/IGVFFI9706EHIQ/@@download/IGVFFI9706EHIQ.fastq.gz",
"md5sum": "62b5370bf1fdaffe26ab71f7ec18db46",
"s3_uri": "s3://igvf-files/2023/09/05/80cddb34-3e61-4118-8292-b91a7308929a/IGVFFI9706EHIQ.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-154_L1_SS-PKR-129_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5709RHHR/",
"accession": "IGVFFI5709RHHR",
"aliases": [
"bradley-bernstein:SS-LS_2029_R1",
"bradley-bernstein:SS-LS_243_R1",
"buenrostro-bernstein:SS-LS_2029_R1",
"buenrostro-bernstein:SS-LS_243_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-09-05T19:27:56.550305+00:00",
"file_format": "fastq",
"file_size": 231340764,
"href": "/sequence-files/IGVFFI5709RHHR/@@download/IGVFFI5709RHHR.fastq.gz",
"md5sum": "1ef41d11caea97261da98265487f2d80",
"s3_uri": "s3://igvf-files/2023/09/05/0016ced5-a9c9-41df-af5c-ae02226ba9d0/IGVFFI5709RHHR.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-154_L2_SS-PKR-129_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5183LDFN/",
"accession": "IGVFFI5183LDFN",
"aliases": [
"bradley-bernstein:SS-LS_2029_R2",
"bradley-bernstein:SS-LS_243_R2",
"buenrostro-bernstein:SS-LS_2029_R2",
"buenrostro-bernstein:SS-LS_243_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-09-05T19:27:57.411059+00:00",
"file_format": "fastq",
"file_size": 411143510,
"href": "/sequence-files/IGVFFI5183LDFN/@@download/IGVFFI5183LDFN.fastq.gz",
"md5sum": "2a039f2e8f382ca37d0c4e0e0fa7dbd1",
"s3_uri": "s3://igvf-files/2023/09/05/61a8a6d7-aca2-4732-a312-481ef1fe0002/IGVFFI5183LDFN.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-154_L2_SS-PKR-129_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9559QEAH/",
"accession": "IGVFFI9559QEAH",
"aliases": [
"bradley-bernstein:SS-LS_2029_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:49:53.673516+00:00",
"file_format": "yaml",
"file_size": 1187,
"href": "/configuration-files/IGVFFI9559QEAH/@@download/IGVFFI9559QEAH.yaml.gz",
"md5sum": "f112b9082ff105c7b02f56b6f8aa12b4",
"s3_uri": "s3://igvf-files/2024/09/17/c0607cd6-06f6-4f74-98b9-5fed7ee22340/IGVFFI9559QEAH.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_2029_seqspecv3.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9026GHLA/",
"accession": "IGVFFI9026GHLA",
"aliases": [
"bradley-bernstein:SS-LS_2001_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:50:00.412489+00:00",
"file_format": "yaml",
"file_size": 1187,
"href": "/configuration-files/IGVFFI9026GHLA/@@download/IGVFFI9026GHLA.yaml.gz",
"md5sum": "9c950c10e8b23db58a84a5304304ff0a",
"s3_uri": "s3://igvf-files/2024/09/17/70295133-2c92-471b-aa90-cc2dfebf95b3/IGVFFI9026GHLA.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_2001_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/IGVFDS4911ZDCJ/",
"accession": "IGVFDS4911ZDCJ",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8535JZRF/",
"accession": "IGVFDS8535JZRF",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8078FJZR/",
"accession": "IGVFDS8078FJZR",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:22:36.939667+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": "2023-09-05T19:27:45.415694+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "2e317a9c-010c-482f-8a46-22a0f7ffb7e1"
}