{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8645IDXO/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8645IDXO",
"aliases": [
"bradley-bernstein:scATAC Lib 117",
"buenrostro-bernstein:scATAC Lib 117"
],
"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 [IGVFSM9781HISX](/tissues/IGVFSM9781HISX/) 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/IGVFSM9781HISX/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS8645IDXO](/measurement-sets/IGVFDS8645IDXO/) 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/IGVFDS8645IDXO/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS8645IDXO](/measurement-sets/IGVFDS8645IDXO/) has in progress subobject tabular file [IGVFFI0400MBIM](/tabular-files/IGVFFI0400MBIM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS8645IDXO/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS8645IDXO](/measurement-sets/IGVFDS8645IDXO/) 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/IGVFDS8645IDXO/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM9781HISX](/tissues/IGVFSM9781HISX/) 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/IGVFSM9781HISX/"
}
]
},
"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": "2023-08-28T19:18:54.522133+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": [
{
"@id": "/sequence-files/IGVFFI0716KABP/",
"accession": "IGVFFI0716KABP",
"aliases": [
"bradley-bernstein:SS-LS_171_R1",
"bradley-bernstein:SS-LS_2106_R1",
"buenrostro-bernstein:SS-LS_171_R1",
"buenrostro-bernstein:SS-LS_2106_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T19:19:23.066511+00:00",
"file_format": "fastq",
"file_size": 1106602378,
"href": "/sequence-files/IGVFFI0716KABP/@@download/IGVFFI0716KABP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/08/28/e2fa0b21-5189-4ea4-a8b3-23b79d37ab2b/IGVFFI0716KABP.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-188_L2_SS-PKR-131_2022-APRIL-R1-PLATE2-ENTIRE-PLATE_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2873EEMS/",
"accession": "IGVFFI2873EEMS",
"aliases": [
"bradley-bernstein:SS-LS_171_R2",
"bradley-bernstein:SS-LS_2106_R2",
"buenrostro-bernstein:SS-LS_171_R2",
"buenrostro-bernstein:SS-LS_2106_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T19:19:24.011345+00:00",
"file_format": "fastq",
"file_size": 1973259711,
"href": "/sequence-files/IGVFFI2873EEMS/@@download/IGVFFI2873EEMS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/08/28/d2cada38-c794-4736-8612-84e82af22057/IGVFFI2873EEMS.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-188_L2_SS-PKR-131_2022-APRIL-R1-PLATE2-ENTIRE-PLATE_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7093KEGU/",
"accession": "IGVFFI7093KEGU",
"aliases": [
"bradley-bernstein:SS-LS_170_R1",
"bradley-bernstein:SS-LS_2059_R1",
"buenrostro-bernstein:SS-LS_170_R1",
"buenrostro-bernstein:SS-LS_2059_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T19:19:21.282484+00:00",
"file_format": "fastq",
"file_size": 1109736627,
"href": "/sequence-files/IGVFFI7093KEGU/@@download/IGVFFI7093KEGU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/08/28/ee49ec0d-6736-4d7d-b87a-ba6684f48468/IGVFFI7093KEGU.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-188_L1_SS-PKR-131_2022-APRIL-R1-PLATE2-ENTIRE-PLATE_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5827ESIJ/",
"accession": "IGVFFI5827ESIJ",
"aliases": [
"bradley-bernstein:SS-LS_170_R2",
"bradley-bernstein:SS-LS_2059_R2",
"buenrostro-bernstein:SS-LS_170_R2",
"buenrostro-bernstein:SS-LS_2059_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T19:19:22.172487+00:00",
"file_format": "fastq",
"file_size": 1982258702,
"href": "/sequence-files/IGVFFI5827ESIJ/@@download/IGVFFI5827ESIJ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/08/28/0c295e9c-7d41-40c6-b2c0-9c4507b3b877/IGVFFI5827ESIJ.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-188_L1_SS-PKR-131_2022-APRIL-R1-PLATE2-ENTIRE-PLATE_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5074EAGI/",
"accession": "IGVFFI5074EAGI",
"aliases": [
"bradley-bernstein:SS-LS_2059_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:49:41.514394+00:00",
"file_format": "yaml",
"file_size": 1190,
"href": "/configuration-files/IGVFFI5074EAGI/@@download/IGVFFI5074EAGI.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/17/e1ba87f7-b455-4266-994f-3e366502a58c/IGVFFI5074EAGI.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_2059_seqspecv3.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9449ARSM/",
"accession": "IGVFFI9449ARSM",
"aliases": [
"bradley-bernstein:SS-LS_2106_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:49:34.594301+00:00",
"file_format": "yaml",
"file_size": 1189,
"href": "/configuration-files/IGVFFI9449ARSM/@@download/IGVFFI9449ARSM.yaml.gz",
"s3_uri": "s3://igvf-files/2024/09/17/31e4bced-9d28-4545-9d8f-c1079d624577/IGVFFI9449ARSM.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_2106_seqspecv3.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4147RERW/"
],
"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/IGVFDS8528TQHC/",
"accession": "IGVFDS8528TQHC",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS0956TMWA/",
"accession": "IGVFDS0956TMWA",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS7709QUBW/",
"accession": "IGVFDS7709QUBW",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4464LQXA/",
"accession": "IGVFDS4464LQXA",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8248GGOY/",
"accession": "IGVFDS8248GGOY",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:22:31.573412+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM9781HISX/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9781HISX",
"aliases": [
"bradley-bernstein:BioSam 4561_SS-PKR 131",
"buenrostro-bernstein:BioSam 4561_SS-PKR 131"
],
"cellular_sub_pool": "SS-PKR 131",
"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 131)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2023-08-28T19:19:21.282484+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "d456efae-6932-4693-8963-494cce99a3b1"
}