{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1036WPFQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1036WPFQ",
"aliases": [
"buenrostro-bernstein:scATAC Lib 1780"
],
"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": "Measurement set [IGVFDS1036WPFQ](/measurement-sets/IGVFDS1036WPFQ/) 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/IGVFDS1036WPFQ/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS1036WPFQ](/measurement-sets/IGVFDS1036WPFQ/) has in progress subobject tabular file [IGVFFI6680XCDT](/tabular-files/IGVFFI6680XCDT/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS1036WPFQ/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS1036WPFQ](/measurement-sets/IGVFDS1036WPFQ/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS1036WPFQ/"
},
{
"category": "NTR term ID",
"detail": "Sample term for [NTR_0000646](/sample-terms/NTR_0000646/) has been newly requested. Ontology terms with a newly requested term ID are expected to have it updated following its addition to the appropriate ontology database.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_ntr_term_id",
"path": "/sample-terms/NTR_0000646/"
},
{
"category": "missing publication",
"detail": "Tissue [IGVFSM1668LOKY](/tissues/IGVFSM1668LOKY/) 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/IGVFSM1668LOKY/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS1036WPFQ](/measurement-sets/IGVFDS1036WPFQ/) 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/IGVFDS1036WPFQ/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM1668LOKY](/tissues/IGVFSM1668LOKY/) 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/IGVFSM1668LOKY/"
}
]
},
"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": "2025-03-05T15:34:02.141097+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO3508PMXX/",
"accession": "IGVFDO3508PMXX",
"aliases": [
"ali-mortazavi:768_B6J_10F",
"buenrostro-bernstein:Donor 2078"
],
"sex": "female",
"status": "released",
"strain_background": "C57BL/6J (B6)",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
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"accession": "IGVFFI8896KLYI",
"aliases": [
"buenrostro-bernstein:SS-LS_8375_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:54:13.255839+00:00",
"file_format": "fastq",
"file_size": 3315236292,
"href": "/sequence-files/IGVFFI8896KLYI/@@download/IGVFFI8896KLYI.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/d87e481f-dd5e-483f-990c-5a0b724bf1c3/IGVFFI8896KLYI.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2255_L4_SS-PKR-605_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5491WVNS/",
"accession": "IGVFFI5491WVNS",
"aliases": [
"buenrostro-bernstein:SS-LS_8395_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:54:57.768108+00:00",
"file_format": "fastq",
"file_size": 4564438972,
"href": "/sequence-files/IGVFFI5491WVNS/@@download/IGVFFI5491WVNS.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/4e73e83d-18c5-46cf-b338-339964154fcb/IGVFFI5491WVNS.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2255_L6_SS-PKR-605_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3761PXJP/",
"accession": "IGVFFI3761PXJP",
"aliases": [
"buenrostro-bernstein:SS-LS_8395_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:54:55.038247+00:00",
"file_format": "fastq",
"file_size": 3315564097,
"href": "/sequence-files/IGVFFI3761PXJP/@@download/IGVFFI3761PXJP.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/abec612d-4b17-47e7-9334-a5e95826d0aa/IGVFFI3761PXJP.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2255_L6_SS-PKR-605_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6307BBYT/",
"accession": "IGVFFI6307BBYT",
"aliases": [
"buenrostro-bernstein:SS-LS_8385_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:54:35.720492+00:00",
"file_format": "fastq",
"file_size": 4561812606,
"href": "/sequence-files/IGVFFI6307BBYT/@@download/IGVFFI6307BBYT.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/83865c36-e831-4bd1-a4b8-0f4e0ae9a242/IGVFFI6307BBYT.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2255_L5_SS-PKR-605_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8157TCKX/",
"accession": "IGVFFI8157TCKX",
"aliases": [
"buenrostro-bernstein:SS-LS_8385_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:54:33.968907+00:00",
"file_format": "fastq",
"file_size": 3314983670,
"href": "/sequence-files/IGVFFI8157TCKX/@@download/IGVFFI8157TCKX.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/0a8e1511-a045-4af1-9859-2b39bcce4b95/IGVFFI8157TCKX.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2255_L5_SS-PKR-605_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0994URAZ/",
"accession": "IGVFFI0994URAZ",
"aliases": [
"buenrostro-bernstein:SS-LS_8375_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:54:15.031191+00:00",
"file_format": "fastq",
"file_size": 4592971031,
"href": "/sequence-files/IGVFFI0994URAZ/@@download/IGVFFI0994URAZ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/81431087-bd2e-47da-b1c1-37109b014235/IGVFFI0994URAZ.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2255_L4_SS-PKR-605_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9919FYIN/",
"accession": "IGVFFI9919FYIN",
"aliases": [
"buenrostro-bernstein:SS-LS_8375_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T20:00:00.993047+00:00",
"file_format": "yaml",
"file_size": 1250,
"href": "/configuration-files/IGVFFI9919FYIN/@@download/IGVFFI9919FYIN.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/2c6d8043-d92e-4594-b771-1f76911b90ef/IGVFFI9919FYIN.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8375_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1447CHHF/",
"accession": "IGVFFI1447CHHF",
"aliases": [
"buenrostro-bernstein:SS-LS_8385_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T20:00:14.956363+00:00",
"file_format": "yaml",
"file_size": 1250,
"href": "/configuration-files/IGVFFI1447CHHF/@@download/IGVFFI1447CHHF.yaml.gz",
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"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8385_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8263GRNS/",
"accession": "IGVFFI8263GRNS",
"aliases": [
"buenrostro-bernstein:SS-LS_8395_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T20:00:25.398474+00:00",
"file_format": "yaml",
"file_size": 1251,
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"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8395_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4479WEBI/"
],
"lab": {
"@id": "/labs/jason-buenrostro/",
"title": "Jason Buenrostro, Broad"
},
"multiome_size": 2,
"onlist_files": [
"/tabular-files/IGVFFI6680XCDT/",
"/tabular-files/IGVFFI2668ZFEB/"
],
"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/IGVFDS2449MQOK/",
"accession": "IGVFDS2449MQOK",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:21:44.644988+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM1668LOKY/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1668LOKY",
"aliases": [
"buenrostro-bernstein:BioSam 5155_SS-PKR 605"
],
"cellular_sub_pool": "SS-PKR 605",
"classifications": [
"tissue"
],
"institutional_certificates": [],
"sample_terms": [
{
"@id": "/sample-terms/NTR_0000646/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "left cerebral cortex",
"term_name": "left cerebral cortex"
}
],
"status": "released",
"summary": "Mus musculus C57BL/6J (female) left cerebral cortex tissue (cellular sub pool: SS-PKR 605)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T15:54:13.255839+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "b8e4aeb3-8689-4802-b256-fcfb13d12a98"
}