{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0073HSBP/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0073HSBP",
"aliases": [
"buenrostro-bernstein:scATAC Lib 1777"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002764/",
"assay_slims": [
"chromatin accessibility"
],
"status": "released",
"term_name": "single-cell ATAC-seq"
},
"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": "Measurement set [IGVFDS0073HSBP](/measurement-sets/IGVFDS0073HSBP/) 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/IGVFDS0073HSBP/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0073HSBP](/measurement-sets/IGVFDS0073HSBP/) has in progress subobject tabular file [IGVFFI3897QKNI](/tabular-files/IGVFFI3897QKNI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0073HSBP/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0073HSBP](/measurement-sets/IGVFDS0073HSBP/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0073HSBP/"
},
{
"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/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS0073HSBP](/measurement-sets/IGVFDS0073HSBP/) 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/IGVFDS0073HSBP/"
}
],
"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": "2025-03-05T15:34:40.186145+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": [
{
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"accession": "IGVFFI0157MFIS",
"aliases": [
"buenrostro-bernstein:SS-LS_8392_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:00:06.881731+00:00",
"file_format": "fastq",
"file_size": 4870582114,
"href": "/sequence-files/IGVFFI0157MFIS/@@download/IGVFFI0157MFIS.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/be7c45a1-2d80-4aef-a88e-39ae2ef2789b/IGVFFI0157MFIS.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-2252_L6_SS-PKR-603_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8737UTHR/",
"accession": "IGVFFI8737UTHR",
"aliases": [
"buenrostro-bernstein:SS-LS_8382_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:59:44.734591+00:00",
"file_format": "fastq",
"file_size": 4843881187,
"href": "/sequence-files/IGVFFI8737UTHR/@@download/IGVFFI8737UTHR.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/060318e2-d69b-44fa-bcd2-9f91c0931b4c/IGVFFI8737UTHR.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-2252_L5_SS-PKR-603_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3637RIIY/",
"accession": "IGVFFI3637RIIY",
"aliases": [
"buenrostro-bernstein:SS-LS_8382_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:59:46.906302+00:00",
"file_format": "fastq",
"file_size": 6906790947,
"href": "/sequence-files/IGVFFI3637RIIY/@@download/IGVFFI3637RIIY.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/39d3e316-ad84-405d-a27e-20b25f041b32/IGVFFI3637RIIY.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-2252_L5_SS-PKR-603_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6351PWLQ/",
"accession": "IGVFFI6351PWLQ",
"aliases": [
"buenrostro-bernstein:SS-LS_8372_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:59:26.947664+00:00",
"file_format": "fastq",
"file_size": 6939914585,
"href": "/sequence-files/IGVFFI6351PWLQ/@@download/IGVFFI6351PWLQ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/0b1bcef2-bb19-43af-90bd-30d71447f52f/IGVFFI6351PWLQ.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-2252_L4_SS-PKR-603_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2382SHLK/",
"accession": "IGVFFI2382SHLK",
"aliases": [
"buenrostro-bernstein:SS-LS_8372_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:59:24.910572+00:00",
"file_format": "fastq",
"file_size": 4838602816,
"href": "/sequence-files/IGVFFI2382SHLK/@@download/IGVFFI2382SHLK.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/6c575a33-7cd1-4712-8d8d-72a70e2ee9f1/IGVFFI2382SHLK.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-2252_L4_SS-PKR-603_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9951VBJS/",
"accession": "IGVFFI9951VBJS",
"aliases": [
"buenrostro-bernstein:SS-LS_8392_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:00:09.090851+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI9951VBJS/@@download/IGVFFI9951VBJS.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/39b7ffdb-6963-42e7-a052-af9cf84d6a04/IGVFFI9951VBJS.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-2252_L6_SS-PKR-603_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4429LRUN/",
"accession": "IGVFFI4429LRUN",
"aliases": [
"buenrostro-bernstein:SS-LS_8372_seqspec"
],
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"creation_timestamp": "2025-03-07T20:01:15.966812+00:00",
"file_format": "yaml",
"file_size": 1255,
"href": "/configuration-files/IGVFFI4429LRUN/@@download/IGVFFI4429LRUN.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/104fe732-c4d3-4f22-ad3c-fe74728c3788/IGVFFI4429LRUN.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8372_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5264TNUW/",
"accession": "IGVFFI5264TNUW",
"aliases": [
"buenrostro-bernstein:SS-LS_8392_seqspec"
],
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"creation_timestamp": "2025-03-07T20:01:37.367404+00:00",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3752VDCM/",
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"buenrostro-bernstein:SS-LS_8382_seqspec"
],
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"creation_timestamp": "2025-03-07T20:01:25.837380+00:00",
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"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8382_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": "product",
"preferred_assay_title": "SHARE-seq",
"protocols": [
"https://www.protocols.io/view/share-seq-protocol-v2-2-di3y4gpw"
],
"related_multiome_datasets": [
{
"@id": "/measurement-sets/IGVFDS0524UJOI/",
"accession": "IGVFDS0524UJOI",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:22:01.882371+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM1833ODAY/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1833ODAY",
"aliases": [
"buenrostro-bernstein:BioSam 5148_SS-PKR 603"
],
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"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": {
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},
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"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "2f4b5d4c-0a33-49b6-8bb5-23b0813cd32c"
}