{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7489XUHT/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7489XUHT",
"aliases": [
"bradley-bernstein:scATAC Lib 30",
"buenrostro-bernstein:scATAC Lib 30"
],
"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 [IGVFSM7298SRFZ](/primary-cells/IGVFSM7298SRFZ/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/primary-cells/IGVFSM7298SRFZ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7489XUHT](/measurement-sets/IGVFDS7489XUHT/) has sequence file(s): [IGVFFI9552GZTG](/sequence-files/IGVFFI9552GZTG/), [IGVFFI9073NGEQ](/sequence-files/IGVFFI9073NGEQ/), [IGVFFI0334AIRB](/sequence-files/IGVFFI0334AIRB/), [IGVFFI7318BZTU](/sequence-files/IGVFFI7318BZTU/), [IGVFFI2315HJOV](/sequence-files/IGVFFI2315HJOV/), [IGVFFI5894GJMU](/sequence-files/IGVFFI5894GJMU/), [IGVFFI7945FZLT](/sequence-files/IGVFFI7945FZLT/), [IGVFFI0055JJMO](/sequence-files/IGVFFI0055JJMO/), [IGVFFI6395DAHW](/sequence-files/IGVFFI6395DAHW/), [IGVFFI3582GKYR](/sequence-files/IGVFFI3582GKYR/), [IGVFFI5560XKVN](/sequence-files/IGVFFI5560XKVN/), [IGVFFI3355BLWA](/sequence-files/IGVFFI3355BLWA/), [IGVFFI3827OBNJ](/sequence-files/IGVFFI3827OBNJ/), [IGVFFI8415OCOG](/sequence-files/IGVFFI8415OCOG/), [IGVFFI1205OIAI](/sequence-files/IGVFFI1205OIAI/), [IGVFFI0995UWOW](/sequence-files/IGVFFI0995UWOW/) 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/IGVFDS7489XUHT/"
}
],
"WARNING": [
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS7489XUHT](/measurement-sets/IGVFDS7489XUHT/) 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/IGVFDS7489XUHT/"
}
]
},
"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": "2024-02-12T21:13:16.288218+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO8099ZPMK/",
"accession": "IGVFDO8099ZPMK",
"aliases": [
"bradley-bernstein:Donor 1507",
"buenrostro-bernstein:Donor 1507"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI9552GZTG/",
"accession": "IGVFFI9552GZTG",
"aliases": [
"bradley-bernstein:SS-LS_1529_R2",
"buenrostro-bernstein:SS-LS_1529_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:47:57.418328+00:00",
"file_format": "fastq",
"file_size": 8415,
"href": "/sequence-files/IGVFFI9552GZTG/@@download/IGVFFI9552GZTG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/b951a443-f947-402b-a2af-95e9718151ac/IGVFFI9552GZTG.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-1122_L2_SS-PKR-5_SS-V2-PLATE2-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9073NGEQ/",
"accession": "IGVFFI9073NGEQ",
"aliases": [
"bradley-bernstein:SS-LS_1625_R2",
"buenrostro-bernstein:SS-LS_1625_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:48:37.237301+00:00",
"file_format": "fastq",
"file_size": 7478,
"href": "/sequence-files/IGVFFI9073NGEQ/@@download/IGVFFI9073NGEQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/b87385e4-dc9b-4c9f-8499-be3b54c55d62/IGVFFI9073NGEQ.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-1122_L3_SS-PKR-5_SS-V2-PLATE2-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0334AIRB/",
"accession": "IGVFFI0334AIRB",
"aliases": [
"bradley-bernstein:SS-LS_1529_R1",
"buenrostro-bernstein:SS-LS_1529_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:47:56.460528+00:00",
"file_format": "fastq",
"file_size": 4887,
"href": "/sequence-files/IGVFFI0334AIRB/@@download/IGVFFI0334AIRB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/4775ea80-86c4-41e1-bd35-4839a84b4424/IGVFFI0334AIRB.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-1122_L2_SS-PKR-5_SS-V2-PLATE2-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7318BZTU/",
"accession": "IGVFFI7318BZTU",
"aliases": [
"bradley-bernstein:SS-LS_1433_R1",
"buenrostro-bernstein:SS-LS_1433_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:47:18.241697+00:00",
"file_format": "fastq",
"file_size": 4447,
"href": "/sequence-files/IGVFFI7318BZTU/@@download/IGVFFI7318BZTU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/d973ed13-f24d-41c3-a6b6-969884d5ad41/IGVFFI7318BZTU.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-1122_L1_SS-PKR-5_SS-V2-PLATE2-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2315HJOV/",
"accession": "IGVFFI2315HJOV",
"aliases": [
"bradley-bernstein:SS-LS_1433_R2",
"buenrostro-bernstein:SS-LS_1433_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:47:19.211792+00:00",
"file_format": "fastq",
"file_size": 7661,
"href": "/sequence-files/IGVFFI2315HJOV/@@download/IGVFFI2315HJOV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/dba3695e-a2b0-4e22-9451-9a595799c429/IGVFFI2315HJOV.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-1122_L1_SS-PKR-5_SS-V2-PLATE2-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5894GJMU/",
"accession": "IGVFFI5894GJMU",
"aliases": [
"bradley-bernstein:SS-LS_1625_R1",
"buenrostro-bernstein:SS-LS_1625_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:48:35.260152+00:00",
"file_format": "fastq",
"file_size": 4397,
"href": "/sequence-files/IGVFFI5894GJMU/@@download/IGVFFI5894GJMU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/21658b72-7810-42d2-baad-52ba05d2e52c/IGVFFI5894GJMU.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-1122_L3_SS-PKR-5_SS-V2-PLATE2-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7945FZLT/",
"accession": "IGVFFI7945FZLT",
"aliases": [
"bradley-bernstein:SS-LS_1721_R2",
"buenrostro-bernstein:SS-LS_1721_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:49:15.780939+00:00",
"file_format": "fastq",
"file_size": 8411,
"href": "/sequence-files/IGVFFI7945FZLT/@@download/IGVFFI7945FZLT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/7ef85f7b-bbbe-45b6-b6f0-71f6aaae343c/IGVFFI7945FZLT.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-1122_L4_SS-PKR-5_SS-V2-PLATE2-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0055JJMO/",
"accession": "IGVFFI0055JJMO",
"aliases": [
"bradley-bernstein:SS-LS_2583_R2",
"buenrostro-bernstein:SS-LS_2583_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:52:14.134736+00:00",
"file_format": "fastq",
"file_size": 907131252,
"href": "/sequence-files/IGVFFI0055JJMO/@@download/IGVFFI0055JJMO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/b12bef12-ecbd-417a-9acd-bb65a698da85/IGVFFI0055JJMO.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-59_L4_SS-PKR-5_SS-V2-PLATE2-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6395DAHW/",
"accession": "IGVFFI6395DAHW",
"aliases": [
"bradley-bernstein:SS-LS_2295_R2",
"buenrostro-bernstein:SS-LS_2295_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:50:18.502945+00:00",
"file_format": "fastq",
"file_size": 914821057,
"href": "/sequence-files/IGVFFI6395DAHW/@@download/IGVFFI6395DAHW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/2c54c7b3-a8a8-4eee-893b-1f0c266d4c38/IGVFFI6395DAHW.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-59_L1_SS-PKR-5_SS-V2-PLATE2-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3582GKYR/",
"accession": "IGVFFI3582GKYR",
"aliases": [
"bradley-bernstein:SS-LS_2391_R2",
"buenrostro-bernstein:SS-LS_2391_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:50:55.826764+00:00",
"file_format": "fastq",
"file_size": 919009310,
"href": "/sequence-files/IGVFFI3582GKYR/@@download/IGVFFI3582GKYR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/2a5cf452-6b64-4b34-ba09-ed3bfa409583/IGVFFI3582GKYR.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-59_L2_SS-PKR-5_SS-V2-PLATE2-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5560XKVN/",
"accession": "IGVFFI5560XKVN",
"aliases": [
"bradley-bernstein:SS-LS_2583_R1",
"buenrostro-bernstein:SS-LS_2583_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:52:13.071485+00:00",
"file_format": "fastq",
"file_size": 526020063,
"href": "/sequence-files/IGVFFI5560XKVN/@@download/IGVFFI5560XKVN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/fb9a0029-7a3e-42a7-b0ca-f7180eecda9c/IGVFFI5560XKVN.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-59_L4_SS-PKR-5_SS-V2-PLATE2-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3355BLWA/",
"accession": "IGVFFI3355BLWA",
"aliases": [
"bradley-bernstein:SS-LS_1721_R1",
"buenrostro-bernstein:SS-LS_1721_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:49:14.836608+00:00",
"file_format": "fastq",
"file_size": 4854,
"href": "/sequence-files/IGVFFI3355BLWA/@@download/IGVFFI3355BLWA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/600172b1-263a-4ed6-aca2-9a2084ef2ef0/IGVFFI3355BLWA.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-1122_L4_SS-PKR-5_SS-V2-PLATE2-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3827OBNJ/",
"accession": "IGVFFI3827OBNJ",
"aliases": [
"bradley-bernstein:SS-LS_2295_R1",
"buenrostro-bernstein:SS-LS_2295_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:50:17.561317+00:00",
"file_format": "fastq",
"file_size": 530125208,
"href": "/sequence-files/IGVFFI3827OBNJ/@@download/IGVFFI3827OBNJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/ec27c9b3-39f8-41a1-9dc4-85bf32f2f051/IGVFFI3827OBNJ.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-59_L1_SS-PKR-5_SS-V2-PLATE2-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8415OCOG/",
"accession": "IGVFFI8415OCOG",
"aliases": [
"bradley-bernstein:SS-LS_2391_R1",
"buenrostro-bernstein:SS-LS_2391_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:50:54.772546+00:00",
"file_format": "fastq",
"file_size": 533110413,
"href": "/sequence-files/IGVFFI8415OCOG/@@download/IGVFFI8415OCOG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/abaf4fe3-6fdb-4cb7-97bb-fb8d2a472287/IGVFFI8415OCOG.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-59_L2_SS-PKR-5_SS-V2-PLATE2-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1205OIAI/",
"accession": "IGVFFI1205OIAI",
"aliases": [
"bradley-bernstein:SS-LS_2487_R1",
"buenrostro-bernstein:SS-LS_2487_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:51:32.089816+00:00",
"file_format": "fastq",
"file_size": 531011978,
"href": "/sequence-files/IGVFFI1205OIAI/@@download/IGVFFI1205OIAI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/f777eb17-bb92-4bdb-88d3-9cd1cb73749f/IGVFFI1205OIAI.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-59_L3_SS-PKR-5_SS-V2-PLATE2-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0995UWOW/",
"accession": "IGVFFI0995UWOW",
"aliases": [
"bradley-bernstein:SS-LS_2487_R2",
"buenrostro-bernstein:SS-LS_2487_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:51:32.948055+00:00",
"file_format": "fastq",
"file_size": 913536657,
"href": "/sequence-files/IGVFFI0995UWOW/@@download/IGVFFI0995UWOW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/22e16296-573c-4ac1-a2dd-04163e6860d4/IGVFFI0995UWOW.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-59_L3_SS-PKR-5_SS-V2-PLATE2-3rd-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/IGVFDS1873JMKU/",
"accession": "IGVFDS1873JMKU",
"status": "released"
}
],
"release_timestamp": "2025-01-14T19:03:55.295700+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM7298SRFZ/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7298SRFZ",
"aliases": [
"bradley-bernstein:BioSam 4568_SS-PKR 5",
"buenrostro-bernstein:BioSam 4568_SS-PKR 5"
],
"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 5), male, Homo sapiens (37 years)",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2024-02-12T21:47:18.241697+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "47bd0713-fbc0-459c-a12b-b18180cb1cb9"
}