{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2721AQQO/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2721AQQO",
"aliases": [
"bradley-bernstein:scATAC Lib 625",
"buenrostro-bernstein:scATAC Lib 625"
],
"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 [IGVFDS2721AQQO](/measurement-sets/IGVFDS2721AQQO/) 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/IGVFDS2721AQQO/"
},
{
"category": "mismatched status",
"detail": "Released primary cell [IGVFSM2223HAHK](/primary-cells/IGVFSM2223HAHK/) has in progress subobject source [allcells](/sources/allcells/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/primary-cells/IGVFSM2223HAHK/"
},
{
"category": "missing publication",
"detail": "Primary cell [IGVFSM2223HAHK](/primary-cells/IGVFSM2223HAHK/) 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": "/primary-cells/IGVFSM2223HAHK/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS2721AQQO](/measurement-sets/IGVFDS2721AQQO/) has a sequence file [IGVFFI3567OWKU](/sequence-files/IGVFFI3567OWKU/) missing `read_names`. Sequence files are expected to have read names.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_single_cell_read_names",
"path": "/measurement-sets/IGVFDS2721AQQO/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS2721AQQO](/measurement-sets/IGVFDS2721AQQO/) has a sequence file [IGVFFI0371QDGZ](/sequence-files/IGVFFI0371QDGZ/) missing `read_names`. Sequence files are expected to have read names.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_single_cell_read_names",
"path": "/measurement-sets/IGVFDS2721AQQO/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS2721AQQO](/measurement-sets/IGVFDS2721AQQO/) has a sequence file [IGVFFI8305JJZD](/sequence-files/IGVFFI8305JJZD/) missing `read_names`. Sequence files are expected to have read names.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_single_cell_read_names",
"path": "/measurement-sets/IGVFDS2721AQQO/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS2721AQQO](/measurement-sets/IGVFDS2721AQQO/) has a sequence file [IGVFFI1456HVZR](/sequence-files/IGVFFI1456HVZR/) missing `read_names`. Sequence files are expected to have read names.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_single_cell_read_names",
"path": "/measurement-sets/IGVFDS2721AQQO/"
},
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS2721AQQO](/measurement-sets/IGVFDS2721AQQO/) has an `assay_term` of single-cell ATAC-seq but no `onlist_files` nor `onlist_methods`. Measurement sets to be processed via the single cell uniform pipeline are expected to have onlist files and onlist methods indicated.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_onlist",
"path": "/measurement-sets/IGVFDS2721AQQO/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM2223HAHK](/primary-cells/IGVFSM2223HAHK/) 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": "/primary-cells/IGVFSM2223HAHK/"
}
]
},
"award": {
"@id": "/awards/HG011986/",
"component": "mapping",
"contact_pi": {
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"title": "Jason Buenrostro"
},
"title": "A foundational resource of functional elements, TF footprints and gene regulatory interactions"
},
"control_for": [],
"controlled_access": false,
"creation_timestamp": "2023-10-30T18:36:52.800301+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
"@id": "/human-donors/IGVFDO0609CPVJ/",
"accession": "IGVFDO0609CPVJ",
"aliases": [
"bradley-bernstein:Donor 1992",
"buenrostro-bernstein:Donor 1992"
],
"sex": "unspecified",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
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"accession": "IGVFFI3567OWKU",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-10-30T18:37:15.705804+00:00",
"file_format": "fastq",
"file_size": 6434043860,
"href": "/sequence-files/IGVFFI3567OWKU/@@download/IGVFFI3567OWKU.fastq.gz",
"md5sum": "d90c8a35abe92070fd4b19645a96b084",
"s3_uri": "s3://igvf-files/2023/10/30/7555d582-f2a9-4868-9dd3-6f1dd1df74ab/IGVFFI3567OWKU.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0371QDGZ/",
"accession": "IGVFFI0371QDGZ",
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-10-30T18:37:16.562982+00:00",
"file_format": "fastq",
"file_size": 10494576406,
"href": "/sequence-files/IGVFFI0371QDGZ/@@download/IGVFFI0371QDGZ.fastq.gz",
"md5sum": "1c2c130fceddb4838cf7b624145f52a6",
"s3_uri": "s3://igvf-files/2023/10/30/6cb2e3c0-a267-4310-aefb-d805d756e136/IGVFFI0371QDGZ.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://fc-7b87fd5f-6af3-4823-befa-ac5875469fa1/BMMC_single_donor_ATAC_L002_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8305JJZD/",
"accession": "IGVFFI8305JJZD",
"aliases": [
"bradley-bernstein:SS-LS_174_R1",
"buenrostro-bernstein:SS-LS_174_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-10-30T18:37:17.608106+00:00",
"file_format": "fastq",
"file_size": 5589440271,
"href": "/sequence-files/IGVFFI8305JJZD/@@download/IGVFFI8305JJZD.fastq.gz",
"md5sum": "3bc3a2b2fff18639514f76be143eff11",
"s3_uri": "s3://igvf-files/2023/10/30/432ea2e7-a41a-4ca5-a669-2f4fb61fa1a1/IGVFFI8305JJZD.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq 6000"
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"status": "released",
"submitted_file_name": "gs://fc-7b87fd5f-6af3-4823-befa-ac5875469fa1/BMMC_single_donor_ATAC_L001_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1456HVZR/",
"accession": "IGVFFI1456HVZR",
"aliases": [
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"buenrostro-bernstein:SS-LS_174_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-10-30T18:37:18.460222+00:00",
"file_format": "fastq",
"file_size": 9104962588,
"href": "/sequence-files/IGVFFI1456HVZR/@@download/IGVFFI1456HVZR.fastq.gz",
"md5sum": "8c7854bde45c89c434665f7518155a5d",
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"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
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"submitted_file_name": "gs://fc-7b87fd5f-6af3-4823-befa-ac5875469fa1/BMMC_single_donor_ATAC_L001_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8765LWAH/",
"accession": "IGVFFI8765LWAH",
"aliases": [
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],
"content_type": "seqspec",
"creation_timestamp": "2024-11-21T19:14:21.523579+00:00",
"file_format": "yaml",
"file_size": 1209,
"href": "/configuration-files/IGVFFI8765LWAH/@@download/IGVFFI8765LWAH.yaml.gz",
"md5sum": "f5982cc505aca385c9ea9e0749a6bee8",
"s3_uri": "s3://igvf-files/2024/11/21/5e447701-923b-4c64-89fb-e9df76d14edf/IGVFFI8765LWAH.yaml.gz",
"status": "revoked",
"submitted_file_name": "/Users/swekhand/Documents/GitHub/epi-sw-IGVF-submission/submissions/seqspecs/sai-single-donor-atac-upgraded/SS-LS_175_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9435UFOD/",
"accession": "IGVFFI9435UFOD",
"aliases": [
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],
"content_type": "seqspec",
"creation_timestamp": "2024-11-21T19:14:23.369724+00:00",
"file_format": "yaml",
"file_size": 1207,
"href": "/configuration-files/IGVFFI9435UFOD/@@download/IGVFFI9435UFOD.yaml.gz",
"md5sum": "c53b74d049928cec328417334498570f",
"s3_uri": "s3://igvf-files/2024/11/21/fd7d5b30-468c-4ac0-8606-9967323fdb35/IGVFFI9435UFOD.yaml.gz",
"status": "revoked",
"submitted_file_name": "/Users/swekhand/Documents/GitHub/epi-sw-IGVF-submission/submissions/seqspecs/sai-single-donor-atac-upgraded/SS-LS_174_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9901DVKV/",
"accession": "IGVFFI9901DVKV",
"aliases": [
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],
"content_type": "seqspec",
"creation_timestamp": "2025-04-14T19:12:53.279535+00:00",
"file_format": "yaml",
"file_size": 1215,
"href": "/configuration-files/IGVFFI9901DVKV/@@download/IGVFFI9901DVKV.yaml.gz",
"md5sum": "36e375f5c5b22b26fa5cd704d1a7f7b6",
"s3_uri": "s3://igvf-files/2025/04/14/2c75c191-3a3b-483e-8f8d-1dc0325958f4/IGVFFI9901DVKV.yaml.gz",
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"submitted_file_name": "/Users/swekhand/Documents/GitHub/epi-sw-IGVF-submission/submissions/seqspecs/sai-single-donor-atac-upgraded/SS-LS_175_seqspec.yaml.gz",
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},
{
"@id": "/configuration-files/IGVFFI4808GAIJ/",
"accession": "IGVFFI4808GAIJ",
"aliases": [
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"content_type": "seqspec",
"creation_timestamp": "2025-04-14T19:12:54.643354+00:00",
"file_format": "yaml",
"file_size": 1214,
"href": "/configuration-files/IGVFFI4808GAIJ/@@download/IGVFFI4808GAIJ.yaml.gz",
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"s3_uri": "s3://igvf-files/2025/04/14/ae47bc64-3218-40f4-881c-d6bcd79f0448/IGVFFI4808GAIJ.yaml.gz",
"status": "released",
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],
"input_for": [
"/analysis-sets/IGVFDS5278IBSB/"
],
"lab": {
"@id": "/labs/jason-buenrostro/",
"title": "Jason Buenrostro, Broad"
},
"multiome_size": 2,
"notes": "Preferred_assay_titles enum SHARE-Seq has been renamed to be SHARE-seq.",
"preferred_assay_title": "SHARE-seq",
"protocols": [
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],
"related_multiome_datasets": [
{
"@id": "/measurement-sets/IGVFDS6911ZLIV/",
"accession": "IGVFDS6911ZLIV",
"status": "released"
}
],
"release_timestamp": "2025-01-14T18:00:13.869255+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM2223HAHK/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2223HAHK",
"aliases": [
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],
"cellular_sub_pool": "SS-PKR 212",
"classifications": [
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],
"institutional_certificates": [
{
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"certificate_identifier": "IP113-25",
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"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/UBERON_0002371/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "bone marrow",
"term_name": "bone marrow"
}
],
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"summary": "Homo sapiens bone marrow cell (cellular sub pool: SS-PKR 212)",
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}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
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"submitted_files_timestamp": "2023-10-30T18:37:15.705804+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "7e688230-c38f-4976-ab16-5346b26f84c0"
}