{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0858CFYH/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0858CFYH",
"aliases": [
"bradley-bernstein:scATAC Lib 32",
"buenrostro-bernstein:scATAC Lib 32"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002764/",
"status": "released",
"term_name": "single-cell ATAC-seq"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released primary cell [IGVFSM5211IRON](/primary-cells/IGVFSM5211IRON/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/primary-cells/IGVFSM5211IRON/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0858CFYH](/measurement-sets/IGVFDS0858CFYH/) has sequence file(s): [IGVFFI5289QYDZ](/sequence-files/IGVFFI5289QYDZ/), [IGVFFI6640AMNH](/sequence-files/IGVFFI6640AMNH/), [IGVFFI2534UYEO](/sequence-files/IGVFFI2534UYEO/), [IGVFFI0212ZEVK](/sequence-files/IGVFFI0212ZEVK/), [IGVFFI0797KPTV](/sequence-files/IGVFFI0797KPTV/), [IGVFFI4333PWXH](/sequence-files/IGVFFI4333PWXH/), [IGVFFI9038ULYA](/sequence-files/IGVFFI9038ULYA/), [IGVFFI3142EPIE](/sequence-files/IGVFFI3142EPIE/), [IGVFFI8784VAFE](/sequence-files/IGVFFI8784VAFE/), [IGVFFI9158AKSJ](/sequence-files/IGVFFI9158AKSJ/), [IGVFFI6116ZKHK](/sequence-files/IGVFFI6116ZKHK/), [IGVFFI4490PDCQ](/sequence-files/IGVFFI4490PDCQ/), [IGVFFI3830KYPB](/sequence-files/IGVFFI3830KYPB/), [IGVFFI3858FHCV](/sequence-files/IGVFFI3858FHCV/), [IGVFFI7898BYAA](/sequence-files/IGVFFI7898BYAA/), [IGVFFI5382SUPE](/sequence-files/IGVFFI5382SUPE/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS0858CFYH/"
}
],
"WARNING": [
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS0858CFYH](/measurement-sets/IGVFDS0858CFYH/) 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": 40,
"level_name": "WARNING",
"name": "audit_onlist",
"path": "/measurement-sets/IGVFDS0858CFYH/"
}
]
},
"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": "2024-02-12T21:12:36.236194+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO2605CUSL/",
"accession": "IGVFDO2605CUSL",
"aliases": [
"bradley-bernstein:Donor 1508",
"buenrostro-bernstein:Donor 1508"
],
"sex": "female",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI5289QYDZ/",
"accession": "IGVFFI5289QYDZ",
"aliases": [
"bradley-bernstein:SS-LS_1533_R1",
"buenrostro-bernstein:SS-LS_1533_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:26:09.448227+00:00",
"file_format": "fastq",
"file_size": 42930,
"href": "/sequence-files/IGVFFI5289QYDZ/@@download/IGVFFI5289QYDZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/8df4d05d-5eda-4843-afd9-2f40a9249f46/IGVFFI5289QYDZ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-1126_L2_SS-PKR-6_SS-V1-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6640AMNH/",
"accession": "IGVFFI6640AMNH",
"aliases": [
"bradley-bernstein:SS-LS_1437_R2",
"buenrostro-bernstein:SS-LS_1437_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:25:32.563087+00:00",
"file_format": "fastq",
"file_size": 88819,
"href": "/sequence-files/IGVFFI6640AMNH/@@download/IGVFFI6640AMNH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/a365fd41-e147-4cd6-9c64-8e3937d1b7b7/IGVFFI6640AMNH.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-1126_L1_SS-PKR-6_SS-V1-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2534UYEO/",
"accession": "IGVFFI2534UYEO",
"aliases": [
"bradley-bernstein:SS-LS_2299_R2",
"buenrostro-bernstein:SS-LS_2299_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:28:21.565073+00:00",
"file_format": "fastq",
"file_size": 693008847,
"href": "/sequence-files/IGVFFI2534UYEO/@@download/IGVFFI2534UYEO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/a5cf7eee-9893-4b31-8426-ee6f8ec9db89/IGVFFI2534UYEO.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-63_L1_SS-PKR-6_SS-V1-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0212ZEVK/",
"accession": "IGVFFI0212ZEVK",
"aliases": [
"bradley-bernstein:SS-LS_2395_R1",
"buenrostro-bernstein:SS-LS_2395_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:28:55.404801+00:00",
"file_format": "fastq",
"file_size": 407988749,
"href": "/sequence-files/IGVFFI0212ZEVK/@@download/IGVFFI0212ZEVK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/06336c9f-6001-44da-952b-747c64292fb5/IGVFFI0212ZEVK.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-63_L2_SS-PKR-6_SS-V1-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0797KPTV/",
"accession": "IGVFFI0797KPTV",
"aliases": [
"bradley-bernstein:SS-LS_2395_R2",
"buenrostro-bernstein:SS-LS_2395_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:28:56.370329+00:00",
"file_format": "fastq",
"file_size": 697805565,
"href": "/sequence-files/IGVFFI0797KPTV/@@download/IGVFFI0797KPTV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/c5b1932d-f0c1-4d67-a500-0be9bcdd1dc2/IGVFFI0797KPTV.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-63_L2_SS-PKR-6_SS-V1-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4333PWXH/",
"accession": "IGVFFI4333PWXH",
"aliases": [
"bradley-bernstein:SS-LS_1533_R2",
"buenrostro-bernstein:SS-LS_1533_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:26:10.496145+00:00",
"file_format": "fastq",
"file_size": 92530,
"href": "/sequence-files/IGVFFI4333PWXH/@@download/IGVFFI4333PWXH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/e1237c5d-674b-4899-9a37-d089b3dba607/IGVFFI4333PWXH.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-1126_L2_SS-PKR-6_SS-V1-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9038ULYA/",
"accession": "IGVFFI9038ULYA",
"aliases": [
"bradley-bernstein:SS-LS_1437_R1",
"buenrostro-bernstein:SS-LS_1437_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:25:31.606632+00:00",
"file_format": "fastq",
"file_size": 41453,
"href": "/sequence-files/IGVFFI9038ULYA/@@download/IGVFFI9038ULYA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/d766c136-06bc-45e4-9b91-e26bd417c781/IGVFFI9038ULYA.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-1126_L1_SS-PKR-6_SS-V1-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3142EPIE/",
"accession": "IGVFFI3142EPIE",
"aliases": [
"bradley-bernstein:SS-LS_2587_R2",
"buenrostro-bernstein:SS-LS_2587_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:30:13.272658+00:00",
"file_format": "fastq",
"file_size": 690117714,
"href": "/sequence-files/IGVFFI3142EPIE/@@download/IGVFFI3142EPIE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/57a2e755-6388-4801-a377-1fcde5907a50/IGVFFI3142EPIE.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-63_L4_SS-PKR-6_SS-V1-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8784VAFE/",
"accession": "IGVFFI8784VAFE",
"aliases": [
"bradley-bernstein:SS-LS_1725_R1",
"buenrostro-bernstein:SS-LS_1725_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:27:21.003165+00:00",
"file_format": "fastq",
"file_size": 40975,
"href": "/sequence-files/IGVFFI8784VAFE/@@download/IGVFFI8784VAFE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/5cacd0c6-a52e-4c97-930c-01337995d60b/IGVFFI8784VAFE.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-1126_L4_SS-PKR-6_SS-V1-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9158AKSJ/",
"accession": "IGVFFI9158AKSJ",
"aliases": [
"bradley-bernstein:SS-LS_1629_R1",
"buenrostro-bernstein:SS-LS_1629_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:26:46.481009+00:00",
"file_format": "fastq",
"file_size": 40524,
"href": "/sequence-files/IGVFFI9158AKSJ/@@download/IGVFFI9158AKSJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/74a664db-fa12-48d2-8a65-161a8daf090b/IGVFFI9158AKSJ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-1126_L3_SS-PKR-6_SS-V1-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6116ZKHK/",
"accession": "IGVFFI6116ZKHK",
"aliases": [
"bradley-bernstein:SS-LS_1629_R2",
"buenrostro-bernstein:SS-LS_1629_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:26:47.443937+00:00",
"file_format": "fastq",
"file_size": 86252,
"href": "/sequence-files/IGVFFI6116ZKHK/@@download/IGVFFI6116ZKHK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/c1777f53-5329-4e92-adac-69d3624dcbb3/IGVFFI6116ZKHK.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-1126_L3_SS-PKR-6_SS-V1-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4490PDCQ/",
"accession": "IGVFFI4490PDCQ",
"aliases": [
"bradley-bernstein:SS-LS_1725_R2",
"buenrostro-bernstein:SS-LS_1725_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:27:21.970583+00:00",
"file_format": "fastq",
"file_size": 87773,
"href": "/sequence-files/IGVFFI4490PDCQ/@@download/IGVFFI4490PDCQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/d3c39020-9f06-4ba6-91d9-f554461ea658/IGVFFI4490PDCQ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-1126_L4_SS-PKR-6_SS-V1-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3830KYPB/",
"accession": "IGVFFI3830KYPB",
"aliases": [
"bradley-bernstein:SS-LS_2299_R1",
"buenrostro-bernstein:SS-LS_2299_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:28:20.693052+00:00",
"file_format": "fastq",
"file_size": 404947216,
"href": "/sequence-files/IGVFFI3830KYPB/@@download/IGVFFI3830KYPB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/615eacf1-5129-4ab9-a0c9-4a62ec5b7a50/IGVFFI3830KYPB.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-63_L1_SS-PKR-6_SS-V1-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3858FHCV/",
"accession": "IGVFFI3858FHCV",
"aliases": [
"bradley-bernstein:SS-LS_2587_R1",
"buenrostro-bernstein:SS-LS_2587_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:30:12.319825+00:00",
"file_format": "fastq",
"file_size": 403281422,
"href": "/sequence-files/IGVFFI3858FHCV/@@download/IGVFFI3858FHCV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/a11d4624-f820-4d90-b6eb-c8cbf7b44189/IGVFFI3858FHCV.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-63_L4_SS-PKR-6_SS-V1-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7898BYAA/",
"accession": "IGVFFI7898BYAA",
"aliases": [
"bradley-bernstein:SS-LS_2491_R1",
"buenrostro-bernstein:SS-LS_2491_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:29:33.319593+00:00",
"file_format": "fastq",
"file_size": 406036955,
"href": "/sequence-files/IGVFFI7898BYAA/@@download/IGVFFI7898BYAA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/cf02c3e8-9de0-4f6c-bf19-1eaed1192753/IGVFFI7898BYAA.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-63_L3_SS-PKR-6_SS-V1-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5382SUPE/",
"accession": "IGVFFI5382SUPE",
"aliases": [
"bradley-bernstein:SS-LS_2491_R2",
"buenrostro-bernstein:SS-LS_2491_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:29:34.273197+00:00",
"file_format": "fastq",
"file_size": 693024689,
"href": "/sequence-files/IGVFFI5382SUPE/@@download/IGVFFI5382SUPE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/75270e83-5e14-46de-938f-c97102cab244/IGVFFI5382SUPE.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-63_L3_SS-PKR-6_SS-V1-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
}
],
"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": [
"https://www.protocols.io/view/share-seq-v1-bmbik2ke"
],
"related_multiome_datasets": [
{
"@id": "/measurement-sets/IGVFDS1736NDNN/",
"accession": "IGVFDS1736NDNN",
"status": "released"
}
],
"release_timestamp": "2025-01-14T19:14:10.372969+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM5211IRON/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5211IRON",
"aliases": [
"bradley-bernstein:BioSam 4564_SS-PKR 6",
"buenrostro-bernstein:BioSam 4564_SS-PKR 6"
],
"classifications": [
"primary cell"
],
"sample_terms": [
{
"@id": "/sample-terms/UBERON_0002371/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "bone marrow",
"term_name": "bone marrow"
}
],
"status": "released",
"summary": "bone marrow cell (cellular sub pool: SS-PKR 6), female, Homo sapiens (19 years)",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2024-02-12T21:25:31.606632+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "91698e0f-d5f5-425c-b2ca-7cbc3c2f06bf"
}