{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3074DPDQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3074DPDQ",
"aliases": [
"buenrostro-bernstein:scRNA Lib 842"
],
"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 [IGVFSM7652DCKY](/tissues/IGVFSM7652DCKY/) 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/IGVFSM7652DCKY/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS3074DPDQ](/measurement-sets/IGVFDS3074DPDQ/) 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/IGVFDS3074DPDQ/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS3074DPDQ](/measurement-sets/IGVFDS3074DPDQ/) has in progress subobject tabular file [IGVFFI6680XCDT](/tabular-files/IGVFFI6680XCDT/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS3074DPDQ/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS3074DPDQ](/measurement-sets/IGVFDS3074DPDQ/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS3074DPDQ/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS3074DPDQ](/measurement-sets/IGVFDS3074DPDQ/) 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/IGVFDS3074DPDQ/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM7652DCKY](/tissues/IGVFSM7652DCKY/) 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/IGVFSM7652DCKY/"
}
]
},
"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": "2025-03-05T15:34:07.672345+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": "IGVFFI5363RVGN",
"aliases": [
"buenrostro-bernstein:SS-LS_8413_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:55:32.383772+00:00",
"file_format": "fastq",
"file_size": 4617979194,
"href": "/sequence-files/IGVFFI5363RVGN/@@download/IGVFFI5363RVGN.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/b02e1750-eb36-410e-ac82-261756f689a3/IGVFFI5363RVGN.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-2243_L2_SS-PKR-604_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9047CYME/",
"accession": "IGVFFI9047CYME",
"aliases": [
"buenrostro-bernstein:SS-LS_8423_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:55:56.258476+00:00",
"file_format": "fastq",
"file_size": 7849945673,
"href": "/sequence-files/IGVFFI9047CYME/@@download/IGVFFI9047CYME.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/f6df2fa2-7534-4147-b409-0f3df16cedb1/IGVFFI9047CYME.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
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"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2243_L3_SS-PKR-604_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4840XVFO/",
"accession": "IGVFFI4840XVFO",
"aliases": [
"buenrostro-bernstein:SS-LS_8413_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:55:34.334174+00:00",
"file_format": "fastq",
"file_size": 7828621021,
"href": "/sequence-files/IGVFFI4840XVFO/@@download/IGVFFI4840XVFO.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/a65ac308-5104-41fc-b05c-ae4925a4d1bf/IGVFFI4840XVFO.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-2243_L2_SS-PKR-604_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9309EAFH/",
"accession": "IGVFFI9309EAFH",
"aliases": [
"buenrostro-bernstein:SS-LS_8403_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:55:16.098039+00:00",
"file_format": "fastq",
"file_size": 7890454531,
"href": "/sequence-files/IGVFFI9309EAFH/@@download/IGVFFI9309EAFH.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/ac1203f1-80a9-4ebe-8c45-4a5c8b5b9589/IGVFFI9309EAFH.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-2243_L1_SS-PKR-604_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3787DXQO/",
"accession": "IGVFFI3787DXQO",
"aliases": [
"buenrostro-bernstein:SS-LS_8403_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:55:14.400183+00:00",
"file_format": "fastq",
"file_size": 4644343017,
"href": "/sequence-files/IGVFFI3787DXQO/@@download/IGVFFI3787DXQO.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/fcd8c9e0-05e6-4772-83f4-3db87f66bb3a/IGVFFI3787DXQO.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-2243_L1_SS-PKR-604_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3005GWOJ/",
"accession": "IGVFFI3005GWOJ",
"aliases": [
"buenrostro-bernstein:SS-LS_8423_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:55:54.436282+00:00",
"file_format": "fastq",
"file_size": 4624411435,
"href": "/sequence-files/IGVFFI3005GWOJ/@@download/IGVFFI3005GWOJ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/73a2a370-4c70-438d-9a39-88d3a4522210/IGVFFI3005GWOJ.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-2243_L3_SS-PKR-604_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2644ZPAD/",
"accession": "IGVFFI2644ZPAD",
"aliases": [
"buenrostro-bernstein:SS-LS_8423_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:57:46.760725+00:00",
"file_format": "yaml",
"file_size": 1286,
"href": "/configuration-files/IGVFFI2644ZPAD/@@download/IGVFFI2644ZPAD.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/6f7973f7-886a-4bba-988e-9270fb3d4ee1/IGVFFI2644ZPAD.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8423_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7861SFUL/",
"accession": "IGVFFI7861SFUL",
"aliases": [
"buenrostro-bernstein:SS-LS_8403_seqspec"
],
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"creation_timestamp": "2025-03-07T19:57:25.843302+00:00",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9523QQVP/",
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],
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"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8413_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS7635YNBH/"
],
"lab": {
"@id": "/labs/jason-buenrostro/",
"title": "Jason Buenrostro, Broad"
},
"multiome_size": 2,
"onlist_files": [
"/tabular-files/IGVFFI6680XCDT/",
"/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/IGVFDS9828TNJA/",
"accession": "IGVFDS9828TNJA",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:18:11.152805+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM7652DCKY/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7652DCKY",
"aliases": [
"buenrostro-bernstein:BioSam 5155_SS-PKR 604"
],
"cellular_sub_pool": "SS-PKR 604",
"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 604)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T15:55:14.400183+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "c41ffdbc-c030-4254-b57a-cb7a51e91c13"
}