{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0524UJOI/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0524UJOI",
"aliases": [
"buenrostro-bernstein:scRNA Lib 841"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002631/",
"assay_slims": [
"gene expression"
],
"status": "released",
"term_name": "single-cell RNA sequencing assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"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 [IGVFSM1833ODAY](/tissues/IGVFSM1833ODAY/) 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/IGVFSM1833ODAY/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS0524UJOI](/measurement-sets/IGVFDS0524UJOI/) 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/IGVFDS0524UJOI/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0524UJOI](/measurement-sets/IGVFDS0524UJOI/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0524UJOI/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0524UJOI](/measurement-sets/IGVFDS0524UJOI/) has in progress subobject tabular file [IGVFFI3897QKNI](/tabular-files/IGVFFI3897QKNI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0524UJOI/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS0524UJOI](/measurement-sets/IGVFDS0524UJOI/) 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/IGVFDS0524UJOI/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM1833ODAY](/tissues/IGVFSM1833ODAY/) 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/IGVFSM1833ODAY/"
}
]
},
"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": "2025-03-05T15:34:46.272023+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO8443MWJY/",
"accession": "IGVFDO8443MWJY",
"aliases": [
"ali-mortazavi:773_CASTJ_10M",
"buenrostro-bernstein:Donor 2071"
],
"sex": "male",
"status": "released",
"strain_background": "CAST/EiJ (CAST)",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI7907VISK/",
"accession": "IGVFFI7907VISK",
"aliases": [
"buenrostro-bernstein:SS-LS_8402_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:00:29.805802+00:00",
"file_format": "fastq",
"file_size": 5169029064,
"href": "/sequence-files/IGVFFI7907VISK/@@download/IGVFFI7907VISK.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/9ecb2292-e232-400f-b29d-2c477b4f7559/IGVFFI7907VISK.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-2242_L1_SS-PKR-603_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3291DCPV/",
"accession": "IGVFFI3291DCPV",
"aliases": [
"buenrostro-bernstein:SS-LS_8422_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:01:13.199722+00:00",
"file_format": "fastq",
"file_size": 5158442139,
"href": "/sequence-files/IGVFFI3291DCPV/@@download/IGVFFI3291DCPV.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/38f073d5-78ed-454d-8bb8-6bc74ebaa073/IGVFFI3291DCPV.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-2242_L3_SS-PKR-603_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2326PFJQ/",
"accession": "IGVFFI2326PFJQ",
"aliases": [
"buenrostro-bernstein:SS-LS_8422_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:01:15.500889+00:00",
"file_format": "fastq",
"file_size": 8849565882,
"href": "/sequence-files/IGVFFI2326PFJQ/@@download/IGVFFI2326PFJQ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/cfbe9977-9f14-4239-b2a0-5e193e80ae95/IGVFFI2326PFJQ.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-2242_L3_SS-PKR-603_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2596WAWO/",
"accession": "IGVFFI2596WAWO",
"aliases": [
"buenrostro-bernstein:SS-LS_8412_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:00:51.119016+00:00",
"file_format": "fastq",
"file_size": 5163289425,
"href": "/sequence-files/IGVFFI2596WAWO/@@download/IGVFFI2596WAWO.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/4a9e624d-7652-4d88-a408-78cdde253eed/IGVFFI2596WAWO.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-2242_L2_SS-PKR-603_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9079AJON/",
"accession": "IGVFFI9079AJON",
"aliases": [
"buenrostro-bernstein:SS-LS_8412_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:00:53.035038+00:00",
"file_format": "fastq",
"file_size": 8843072665,
"href": "/sequence-files/IGVFFI9079AJON/@@download/IGVFFI9079AJON.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/09b5aa00-2fc2-4d19-9ce8-dcf956ed583d/IGVFFI9079AJON.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-2242_L2_SS-PKR-603_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3451UYWM/",
"accession": "IGVFFI3451UYWM",
"aliases": [
"buenrostro-bernstein:SS-LS_8402_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:00:31.924027+00:00",
"file_format": "fastq",
"file_size": 8867578570,
"href": "/sequence-files/IGVFFI3451UYWM/@@download/IGVFFI3451UYWM.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/876518ba-f5b7-4359-9a7b-b76c9b80cd90/IGVFFI3451UYWM.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-2242_L1_SS-PKR-603_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8304QFVV/",
"accession": "IGVFFI8304QFVV",
"aliases": [
"buenrostro-bernstein:SS-LS_8402_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:58:41.064157+00:00",
"file_format": "yaml",
"file_size": 1289,
"href": "/configuration-files/IGVFFI8304QFVV/@@download/IGVFFI8304QFVV.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/9e4cdf60-0dd8-4810-9203-e7ed9bacd37f/IGVFFI8304QFVV.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8402_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8029LUIA/",
"accession": "IGVFFI8029LUIA",
"aliases": [
"buenrostro-bernstein:SS-LS_8412_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:58:50.915467+00:00",
"file_format": "yaml",
"file_size": 1287,
"href": "/configuration-files/IGVFFI8029LUIA/@@download/IGVFFI8029LUIA.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/09499006-e66c-45f5-b034-3d2962cc8ed6/IGVFFI8029LUIA.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8412_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4977ATRU/",
"accession": "IGVFFI4977ATRU",
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],
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"creation_timestamp": "2025-03-07T19:59:03.479970+00:00",
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"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8422_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2899TGKG/"
],
"lab": {
"@id": "/labs/jason-buenrostro/",
"title": "Jason Buenrostro, Broad"
},
"multiome_size": 2,
"onlist_files": [
"/tabular-files/IGVFFI3897QKNI/",
"/tabular-files/IGVFFI2668ZFEB/"
],
"onlist_method": "multi",
"preferred_assay_title": "SHARE-seq",
"protocols": [
"https://www.protocols.io/view/share-seq-protocol-v2-2-di3y4gpw"
],
"related_multiome_datasets": [
{
"@id": "/measurement-sets/IGVFDS0073HSBP/",
"accession": "IGVFDS0073HSBP",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:21:52.712425+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM1833ODAY/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1833ODAY",
"aliases": [
"buenrostro-bernstein:BioSam 5148_SS-PKR 603"
],
"cellular_sub_pool": "SS-PKR 603",
"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 CAST/EiJ (male) left cerebral cortex tissue (cellular sub pool: SS-PKR 603)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T16:00:29.805802+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "ace7293e-0893-4cd3-9e56-b3858916412b"
}