{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7747XDUI/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7747XDUI",
"aliases": [
"bradley-bernstein:scATAC Lib 118",
"buenrostro-bernstein:scATAC Lib 118"
],
"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 [IGVFSM8883WYCA](/tissues/IGVFSM8883WYCA/) 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/IGVFSM8883WYCA/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS7747XDUI](/measurement-sets/IGVFDS7747XDUI/) 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/IGVFDS7747XDUI/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS7747XDUI](/measurement-sets/IGVFDS7747XDUI/) has in progress subobject tabular file [IGVFFI0400MBIM](/tabular-files/IGVFFI0400MBIM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS7747XDUI/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS7747XDUI](/measurement-sets/IGVFDS7747XDUI/) 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/IGVFDS7747XDUI/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM8883WYCA](/tissues/IGVFSM8883WYCA/) 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/IGVFSM8883WYCA/"
}
]
},
"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": "2023-08-28T19:09:59.945876+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/IGVFFI9305UBWA/",
"accession": "IGVFFI9305UBWA",
"aliases": [
"bradley-bernstein:SS-LS_2054_R2",
"bradley-bernstein:SS-LS_254_R2",
"buenrostro-bernstein:SS-LS_2054_R2",
"buenrostro-bernstein:SS-LS_254_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T19:11:46.211769+00:00",
"file_format": "fastq",
"file_size": 741587517,
"href": "/sequence-files/IGVFFI9305UBWA/@@download/IGVFFI9305UBWA.fastq.gz",
"md5sum": "0abca91b77eee5df8afd22588dd0e0df",
"s3_uri": "s3://igvf-files/2023/08/28/1a495aa7-f792-46ba-a771-ce1e33bf404b/IGVFFI9305UBWA.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-183_L1_SS-PKR-132_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0137ERGS/",
"accession": "IGVFFI0137ERGS",
"aliases": [
"bradley-bernstein:SS-LS_2101_R1",
"bradley-bernstein:SS-LS_264_R1",
"buenrostro-bernstein:SS-LS_2101_R1",
"buenrostro-bernstein:SS-LS_264_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T19:11:47.151306+00:00",
"file_format": "fastq",
"file_size": 422646530,
"href": "/sequence-files/IGVFFI0137ERGS/@@download/IGVFFI0137ERGS.fastq.gz",
"md5sum": "a63060cc98197f3916cd9fb0f83c09a3",
"s3_uri": "s3://igvf-files/2023/08/28/86596212-facf-4f54-a5ef-5a0d2d4e6196/IGVFFI0137ERGS.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-183_L2_SS-PKR-132_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3119TNSE/",
"accession": "IGVFFI3119TNSE",
"aliases": [
"bradley-bernstein:SS-LS_2101_R2",
"bradley-bernstein:SS-LS_264_R2",
"buenrostro-bernstein:SS-LS_2101_R2",
"buenrostro-bernstein:SS-LS_264_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T19:11:48.070292+00:00",
"file_format": "fastq",
"file_size": 740575330,
"href": "/sequence-files/IGVFFI3119TNSE/@@download/IGVFFI3119TNSE.fastq.gz",
"md5sum": "b79dc9187652b85423aaa7655c8c79cc",
"s3_uri": "s3://igvf-files/2023/08/28/656f4306-023c-4a66-97c7-2b8a481c6aac/IGVFFI3119TNSE.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-183_L2_SS-PKR-132_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9201WYHO/",
"accession": "IGVFFI9201WYHO",
"aliases": [
"bradley-bernstein:SS-LS_2054_R1",
"bradley-bernstein:SS-LS_254_R1",
"buenrostro-bernstein:SS-LS_2054_R1",
"buenrostro-bernstein:SS-LS_254_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T19:11:45.310669+00:00",
"file_format": "fastq",
"file_size": 422466972,
"href": "/sequence-files/IGVFFI9201WYHO/@@download/IGVFFI9201WYHO.fastq.gz",
"md5sum": "e0908e8219e2cc55835445b8d4d0a875",
"s3_uri": "s3://igvf-files/2023/08/28/35b5dcba-3a3b-4b14-bf45-6aa00d70f635/IGVFFI9201WYHO.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-183_L1_SS-PKR-132_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5361AABQ/",
"accession": "IGVFFI5361AABQ",
"aliases": [
"bradley-bernstein:SS-LS_2054_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:49:47.159132+00:00",
"file_format": "yaml",
"file_size": 1188,
"href": "/configuration-files/IGVFFI5361AABQ/@@download/IGVFFI5361AABQ.yaml.gz",
"md5sum": "d581d91431dda912c180e0b8227542cb",
"s3_uri": "s3://igvf-files/2024/09/17/845e739e-2fbe-4785-bb24-2372c0709e2a/IGVFFI5361AABQ.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_2054_seqspecv3.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3071NXZT/",
"accession": "IGVFFI3071NXZT",
"aliases": [
"bradley-bernstein:SS-LS_2101_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:49:40.408480+00:00",
"file_format": "yaml",
"file_size": 1186,
"href": "/configuration-files/IGVFFI3071NXZT/@@download/IGVFFI3071NXZT.yaml.gz",
"md5sum": "2c5101fd114dd25a3152f01cd32ae2dd",
"s3_uri": "s3://igvf-files/2024/09/17/4423896b-4ddd-42eb-b121-511ea79ca430/IGVFFI3071NXZT.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_2101_seqspecv3.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4769QTGM/"
],
"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/IGVFDS9620KXMW/",
"accession": "IGVFDS9620KXMW",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS9728TWXO/",
"accession": "IGVFDS9728TWXO",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6721DTCZ/",
"accession": "IGVFDS6721DTCZ",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8700PWZJ/",
"accession": "IGVFDS8700PWZJ",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4161OUYL/",
"accession": "IGVFDS4161OUYL",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:22:32.608304+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM8883WYCA/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8883WYCA",
"aliases": [
"bradley-bernstein:BioSam 4561_SS-PKR 132",
"buenrostro-bernstein:BioSam 4561_SS-PKR 132"
],
"cellular_sub_pool": "SS-PKR 132",
"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 132)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2023-08-28T19:11:45.310669+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "4003073e-402a-49e7-aee1-712d6c3246da"
}