{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8366JHMT/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8366JHMT",
"aliases": [
"bradley-bernstein:scATAC Lib 37",
"buenrostro-bernstein:scATAC Lib 37"
],
"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 [IGVFSM1533LKGV](/primary-cells/IGVFSM1533LKGV/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/primary-cells/IGVFSM1533LKGV/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8366JHMT](/measurement-sets/IGVFDS8366JHMT/) has sequence file(s): [IGVFFI6311VEUO](/sequence-files/IGVFFI6311VEUO/), [IGVFFI6672IOCB](/sequence-files/IGVFFI6672IOCB/), [IGVFFI4338XYLO](/sequence-files/IGVFFI4338XYLO/), [IGVFFI6711KDFM](/sequence-files/IGVFFI6711KDFM/), [IGVFFI0375LQHB](/sequence-files/IGVFFI0375LQHB/), [IGVFFI4070BKKQ](/sequence-files/IGVFFI4070BKKQ/), [IGVFFI2851QCAV](/sequence-files/IGVFFI2851QCAV/), [IGVFFI9208CMFF](/sequence-files/IGVFFI9208CMFF/), [IGVFFI8121SKYW](/sequence-files/IGVFFI8121SKYW/), [IGVFFI2025UEIK](/sequence-files/IGVFFI2025UEIK/), [IGVFFI8824PLDT](/sequence-files/IGVFFI8824PLDT/), [IGVFFI3034FBSC](/sequence-files/IGVFFI3034FBSC/), [IGVFFI4823EOTK](/sequence-files/IGVFFI4823EOTK/), [IGVFFI3312QKCC](/sequence-files/IGVFFI3312QKCC/), [IGVFFI5030MNUG](/sequence-files/IGVFFI5030MNUG/), [IGVFFI5763NDPY](/sequence-files/IGVFFI5763NDPY/) 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/IGVFDS8366JHMT/"
}
],
"WARNING": [
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS8366JHMT](/measurement-sets/IGVFDS8366JHMT/) 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/IGVFDS8366JHMT/"
}
]
},
"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": "2024-02-12T21:12:27.274238+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO9431XGDA/",
"accession": "IGVFDO9431XGDA",
"aliases": [
"bradley-bernstein:Donor 1506",
"buenrostro-bernstein:Donor 1506"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI6311VEUO/",
"accession": "IGVFFI6311VEUO",
"aliases": [
"bradley-bernstein:SS-LS_1447_R2",
"buenrostro-bernstein:SS-LS_1447_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:23:46.917430+00:00",
"file_format": "fastq",
"file_size": 14336,
"href": "/sequence-files/IGVFFI6311VEUO/@@download/IGVFFI6311VEUO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/06c0f816-60b6-4a00-a0d5-b167ee2eebe6/IGVFFI6311VEUO.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-1136_L1_SS-PKR-7_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6672IOCB/",
"accession": "IGVFFI6672IOCB",
"aliases": [
"bradley-bernstein:SS-LS_1447_R1",
"buenrostro-bernstein:SS-LS_1447_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:23:45.607581+00:00",
"file_format": "fastq",
"file_size": 7104,
"href": "/sequence-files/IGVFFI6672IOCB/@@download/IGVFFI6672IOCB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/29427e7f-b4af-461a-a700-748a6649a24f/IGVFFI6672IOCB.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-1136_L1_SS-PKR-7_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4338XYLO/",
"accession": "IGVFFI4338XYLO",
"aliases": [
"bradley-bernstein:SS-LS_2501_R1",
"buenrostro-bernstein:SS-LS_2501_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:24:20.755657+00:00",
"file_format": "fastq",
"file_size": 637705144,
"href": "/sequence-files/IGVFFI4338XYLO/@@download/IGVFFI4338XYLO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/2054ad9a-bc0e-4f42-aa44-de475b948786/IGVFFI4338XYLO.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-73_L3_SS-PKR-7_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6711KDFM/",
"accession": "IGVFFI6711KDFM",
"aliases": [
"bradley-bernstein:SS-LS_2501_R2",
"buenrostro-bernstein:SS-LS_2501_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:24:21.746210+00:00",
"file_format": "fastq",
"file_size": 1117333980,
"href": "/sequence-files/IGVFFI6711KDFM/@@download/IGVFFI6711KDFM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/1788943a-f608-49d9-b02c-907186b5f1d6/IGVFFI6711KDFM.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-73_L3_SS-PKR-7_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0375LQHB/",
"accession": "IGVFFI0375LQHB",
"aliases": [
"bradley-bernstein:SS-LS_2597_R1",
"buenrostro-bernstein:SS-LS_2597_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:24:58.623191+00:00",
"file_format": "fastq",
"file_size": 633118717,
"href": "/sequence-files/IGVFFI0375LQHB/@@download/IGVFFI0375LQHB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/f8d0c9e3-089c-4745-86be-9b4ee8bb6bf7/IGVFFI0375LQHB.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-73_L4_SS-PKR-7_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4070BKKQ/",
"accession": "IGVFFI4070BKKQ",
"aliases": [
"bradley-bernstein:SS-LS_1543_R1",
"buenrostro-bernstein:SS-LS_1543_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:28:10.296265+00:00",
"file_format": "fastq",
"file_size": 7891,
"href": "/sequence-files/IGVFFI4070BKKQ/@@download/IGVFFI4070BKKQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/5048e0c9-3864-4a05-81f2-00b9c30e7f24/IGVFFI4070BKKQ.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-1136_L2_SS-PKR-7_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2851QCAV/",
"accession": "IGVFFI2851QCAV",
"aliases": [
"bradley-bernstein:SS-LS_2597_R2",
"buenrostro-bernstein:SS-LS_2597_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:24:59.610023+00:00",
"file_format": "fastq",
"file_size": 1112118265,
"href": "/sequence-files/IGVFFI2851QCAV/@@download/IGVFFI2851QCAV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/4ea45caa-6417-45be-a23b-f5c7eaaca679/IGVFFI2851QCAV.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-73_L4_SS-PKR-7_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9208CMFF/",
"accession": "IGVFFI9208CMFF",
"aliases": [
"bradley-bernstein:SS-LS_1543_R2",
"buenrostro-bernstein:SS-LS_1543_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:28:11.426223+00:00",
"file_format": "fastq",
"file_size": 16194,
"href": "/sequence-files/IGVFFI9208CMFF/@@download/IGVFFI9208CMFF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/d9c49148-9d63-4a2f-83bc-0796a9b932d8/IGVFFI9208CMFF.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-1136_L2_SS-PKR-7_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8121SKYW/",
"accession": "IGVFFI8121SKYW",
"aliases": [
"bradley-bernstein:SS-LS_1639_R2",
"buenrostro-bernstein:SS-LS_1639_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:36:32.568209+00:00",
"file_format": "fastq",
"file_size": 12934,
"href": "/sequence-files/IGVFFI8121SKYW/@@download/IGVFFI8121SKYW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/6c82c5b2-c8b4-4a04-814c-01b75aa03577/IGVFFI8121SKYW.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-1136_L3_SS-PKR-7_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2025UEIK/",
"accession": "IGVFFI2025UEIK",
"aliases": [
"bradley-bernstein:SS-LS_1639_R1",
"buenrostro-bernstein:SS-LS_1639_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:36:31.674060+00:00",
"file_format": "fastq",
"file_size": 6628,
"href": "/sequence-files/IGVFFI2025UEIK/@@download/IGVFFI2025UEIK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/0635a090-b92c-498a-bd67-a1e7d6c66a20/IGVFFI2025UEIK.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-1136_L3_SS-PKR-7_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8824PLDT/",
"accession": "IGVFFI8824PLDT",
"aliases": [
"bradley-bernstein:SS-LS_1735_R2",
"buenrostro-bernstein:SS-LS_1735_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:44:58.751256+00:00",
"file_format": "fastq",
"file_size": 12701,
"href": "/sequence-files/IGVFFI8824PLDT/@@download/IGVFFI8824PLDT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/b4b8cec4-dbe3-43f6-930b-be3f561811e8/IGVFFI8824PLDT.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-1136_L4_SS-PKR-7_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3034FBSC/",
"accession": "IGVFFI3034FBSC",
"aliases": [
"bradley-bernstein:SS-LS_1735_R1",
"buenrostro-bernstein:SS-LS_1735_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:44:56.661956+00:00",
"file_format": "fastq",
"file_size": 6324,
"href": "/sequence-files/IGVFFI3034FBSC/@@download/IGVFFI3034FBSC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/b5f59ff3-102e-4761-a702-71d58ac6e64b/IGVFFI3034FBSC.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-1136_L4_SS-PKR-7_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4823EOTK/",
"accession": "IGVFFI4823EOTK",
"aliases": [
"bradley-bernstein:SS-LS_2309_R1",
"buenrostro-bernstein:SS-LS_2309_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:49:38.888877+00:00",
"file_format": "fastq",
"file_size": 636262566,
"href": "/sequence-files/IGVFFI4823EOTK/@@download/IGVFFI4823EOTK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/e2cad65d-6b8e-403c-b00a-0be93affc73b/IGVFFI4823EOTK.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-73_L1_SS-PKR-7_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3312QKCC/",
"accession": "IGVFFI3312QKCC",
"aliases": [
"bradley-bernstein:SS-LS_2309_R2",
"buenrostro-bernstein:SS-LS_2309_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:49:39.830415+00:00",
"file_format": "fastq",
"file_size": 1122193420,
"href": "/sequence-files/IGVFFI3312QKCC/@@download/IGVFFI3312QKCC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/b1e90864-0390-4d3a-802a-d81fc1b376c0/IGVFFI3312QKCC.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-73_L1_SS-PKR-7_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5030MNUG/",
"accession": "IGVFFI5030MNUG",
"aliases": [
"bradley-bernstein:SS-LS_2405_R1",
"buenrostro-bernstein:SS-LS_2405_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:52:57.411104+00:00",
"file_format": "fastq",
"file_size": 638700765,
"href": "/sequence-files/IGVFFI5030MNUG/@@download/IGVFFI5030MNUG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/a3f7f782-f1df-4c5b-bc15-b8d2db2c2bde/IGVFFI5030MNUG.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-73_L2_SS-PKR-7_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5763NDPY/",
"accession": "IGVFFI5763NDPY",
"aliases": [
"bradley-bernstein:SS-LS_2405_R2",
"buenrostro-bernstein:SS-LS_2405_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:52:59.062176+00:00",
"file_format": "fastq",
"file_size": 1121607774,
"href": "/sequence-files/IGVFFI5763NDPY/@@download/IGVFFI5763NDPY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/441f670e-88d6-4bb4-87bb-b7ce315738ab/IGVFFI5763NDPY.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-73_L2_SS-PKR-7_SS-V1-1st-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/IGVFDS1199VPTM/",
"accession": "IGVFDS1199VPTM",
"status": "released"
}
],
"release_timestamp": "2025-01-14T17:52:30.112265+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM1533LKGV/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1533LKGV",
"aliases": [
"bradley-bernstein:BioSam 4563_SS-PKR 7",
"buenrostro-bernstein:BioSam 4563_SS-PKR 7"
],
"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 7), male, Homo sapiens (26 years)",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2024-02-12T21:23:45.607581+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "eba59b8d-e4da-45b8-9066-c35a57003c5a"
}