{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9728TWXO/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9728TWXO",
"aliases": [
"bradley-bernstein:scATAC Lib 119",
"buenrostro-bernstein:scATAC Lib 119"
],
"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 [IGVFDS9728TWXO](/measurement-sets/IGVFDS9728TWXO/) 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/IGVFDS9728TWXO/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS9728TWXO](/measurement-sets/IGVFDS9728TWXO/) has in progress subobject tabular file [IGVFFI0400MBIM](/tabular-files/IGVFFI0400MBIM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS9728TWXO/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS9728TWXO](/measurement-sets/IGVFDS9728TWXO/) 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/IGVFDS9728TWXO/"
}
],
"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": "2023-08-28T19:09:58.424182+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/IGVFFI3794YMRL/",
"accession": "IGVFFI3794YMRL",
"aliases": [
"bradley-bernstein:SS-LS_2055_R1",
"bradley-bernstein:SS-LS_253_R1",
"buenrostro-bernstein:SS-LS_2055_R1",
"buenrostro-bernstein:SS-LS_253_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T19:11:35.665727+00:00",
"file_format": "fastq",
"file_size": 208120096,
"href": "/sequence-files/IGVFFI3794YMRL/@@download/IGVFFI3794YMRL.fastq.gz",
"md5sum": "fd0af26a21ba8fbe7b6b0c35f58abad4",
"s3_uri": "s3://igvf-files/2023/08/28/1875f3e9-8076-42b0-850f-20fbad79f743/IGVFFI3794YMRL.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-184_L1_SS-PKR-132_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2302SLNH/",
"accession": "IGVFFI2302SLNH",
"aliases": [
"bradley-bernstein:SS-LS_2055_R2",
"bradley-bernstein:SS-LS_253_R2",
"buenrostro-bernstein:SS-LS_2055_R2",
"buenrostro-bernstein:SS-LS_253_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T19:11:36.543195+00:00",
"file_format": "fastq",
"file_size": 362395835,
"href": "/sequence-files/IGVFFI2302SLNH/@@download/IGVFFI2302SLNH.fastq.gz",
"md5sum": "5e11f7ef0c550185e2232b7974a7dfc2",
"s3_uri": "s3://igvf-files/2023/08/28/27740dda-66ed-47f2-a48a-34cb1708d62c/IGVFFI2302SLNH.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-184_L1_SS-PKR-132_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4498HQPP/",
"accession": "IGVFFI4498HQPP",
"aliases": [
"bradley-bernstein:SS-LS_2102_R1",
"bradley-bernstein:SS-LS_263_R1",
"buenrostro-bernstein:SS-LS_2102_R1",
"buenrostro-bernstein:SS-LS_263_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T19:11:43.294017+00:00",
"file_format": "fastq",
"file_size": 208458235,
"href": "/sequence-files/IGVFFI4498HQPP/@@download/IGVFFI4498HQPP.fastq.gz",
"md5sum": "b15703e4275591162d6d9496f68d75de",
"s3_uri": "s3://igvf-files/2023/08/28/34ca7788-80e2-4496-aae4-d1836f19cf32/IGVFFI4498HQPP.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-184_L2_SS-PKR-132_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1728ECQN/",
"accession": "IGVFFI1728ECQN",
"aliases": [
"bradley-bernstein:SS-LS_2102_R2",
"bradley-bernstein:SS-LS_263_R2",
"buenrostro-bernstein:SS-LS_2102_R2",
"buenrostro-bernstein:SS-LS_263_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-08-28T19:11:44.371472+00:00",
"file_format": "fastq",
"file_size": 362344435,
"href": "/sequence-files/IGVFFI1728ECQN/@@download/IGVFFI1728ECQN.fastq.gz",
"md5sum": "27f785017aa806f46b4842d28368f426",
"s3_uri": "s3://igvf-files/2023/08/28/b350e57c-ebb7-4ca1-a6ef-a8a81a7c0869/IGVFFI1728ECQN.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-184_L2_SS-PKR-132_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8541ZMMO/",
"accession": "IGVFFI8541ZMMO",
"aliases": [
"bradley-bernstein:SS-LS_2055_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:49:46.025389+00:00",
"file_format": "yaml",
"file_size": 1188,
"href": "/configuration-files/IGVFFI8541ZMMO/@@download/IGVFFI8541ZMMO.yaml.gz",
"md5sum": "ae2ef19ec90d6d930c43f3bf8b33bf0a",
"s3_uri": "s3://igvf-files/2024/09/17/4b3c9bc0-85cf-4e55-a387-c5f7040c7c42/IGVFFI8541ZMMO.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_2055_seqspecv3.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8780JHZV/",
"accession": "IGVFFI8780JHZV",
"aliases": [
"bradley-bernstein:SS-LS_2102_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:49:39.215394+00:00",
"file_format": "yaml",
"file_size": 1187,
"href": "/configuration-files/IGVFFI8780JHZV/@@download/IGVFFI8780JHZV.yaml.gz",
"md5sum": "192597a9442cfbcdf75f4ef79e940d42",
"s3_uri": "s3://igvf-files/2024/09/17/69fc1180-d8ad-4273-8275-1c78555b5456/IGVFFI8780JHZV.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_2102_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/IGVFDS6721DTCZ/",
"accession": "IGVFDS6721DTCZ",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS7747XDUI/",
"accession": "IGVFDS7747XDUI",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8700PWZJ/",
"accession": "IGVFDS8700PWZJ",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4161OUYL/",
"accession": "IGVFDS4161OUYL",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:22:37.970588+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": "2023-08-28T19:11:35.665727+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "4f645625-28d6-49af-8bdd-daf2e21ab772"
}