{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8782BKBI/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8782BKBI",
"aliases": [
"bradley-bernstein:scATAC Lib 42",
"buenrostro-bernstein:scATAC Lib 42"
],
"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 [IGVFSM1494VRXC](/primary-cells/IGVFSM1494VRXC/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/primary-cells/IGVFSM1494VRXC/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8782BKBI](/measurement-sets/IGVFDS8782BKBI/) has sequence file(s): [IGVFFI5527BHCJ](/sequence-files/IGVFFI5527BHCJ/), [IGVFFI2811AYJX](/sequence-files/IGVFFI2811AYJX/), [IGVFFI7526ABSS](/sequence-files/IGVFFI7526ABSS/), [IGVFFI6506WNCM](/sequence-files/IGVFFI6506WNCM/), [IGVFFI0955TCWM](/sequence-files/IGVFFI0955TCWM/), [IGVFFI3595THDP](/sequence-files/IGVFFI3595THDP/), [IGVFFI1130RYAL](/sequence-files/IGVFFI1130RYAL/), [IGVFFI2824HWUQ](/sequence-files/IGVFFI2824HWUQ/), [IGVFFI9275YULT](/sequence-files/IGVFFI9275YULT/), [IGVFFI3574DKQS](/sequence-files/IGVFFI3574DKQS/), [IGVFFI6001NXCF](/sequence-files/IGVFFI6001NXCF/), [IGVFFI9712CUJE](/sequence-files/IGVFFI9712CUJE/), [IGVFFI8604CBGJ](/sequence-files/IGVFFI8604CBGJ/), [IGVFFI2734MPWM](/sequence-files/IGVFFI2734MPWM/), [IGVFFI9431LFUM](/sequence-files/IGVFFI9431LFUM/), [IGVFFI8527DQRD](/sequence-files/IGVFFI8527DQRD/) 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/IGVFDS8782BKBI/"
}
],
"WARNING": [
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS8782BKBI](/measurement-sets/IGVFDS8782BKBI/) 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/IGVFDS8782BKBI/"
}
]
},
"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": "2024-02-12T21:13:18.985581+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/IGVFFI5527BHCJ/",
"accession": "IGVFFI5527BHCJ",
"aliases": [
"bradley-bernstein:SS-LS_1745_R1",
"buenrostro-bernstein:SS-LS_1745_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:49:49.501352+00:00",
"file_format": "fastq",
"file_size": 9294,
"href": "/sequence-files/IGVFFI5527BHCJ/@@download/IGVFFI5527BHCJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/759ab2a3-ae3b-4601-af37-cb6bff74d502/IGVFFI5527BHCJ.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-1146_L4_SS-PKR-7_SS-V2-PLATE2-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2811AYJX/",
"accession": "IGVFFI2811AYJX",
"aliases": [
"bradley-bernstein:SS-LS_1649_R1",
"buenrostro-bernstein:SS-LS_1649_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:48:45.381532+00:00",
"file_format": "fastq",
"file_size": 8822,
"href": "/sequence-files/IGVFFI2811AYJX/@@download/IGVFFI2811AYJX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/c6d87d7f-7dc5-4bfc-94d8-1bdf729208db/IGVFFI2811AYJX.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-1146_L3_SS-PKR-7_SS-V2-PLATE2-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7526ABSS/",
"accession": "IGVFFI7526ABSS",
"aliases": [
"bradley-bernstein:SS-LS_1457_R2",
"buenrostro-bernstein:SS-LS_1457_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:47:29.561874+00:00",
"file_format": "fastq",
"file_size": 17694,
"href": "/sequence-files/IGVFFI7526ABSS/@@download/IGVFFI7526ABSS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/74ac585e-a008-4b60-bf6d-cdac12007cac/IGVFFI7526ABSS.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-1146_L1_SS-PKR-7_SS-V2-PLATE2-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6506WNCM/",
"accession": "IGVFFI6506WNCM",
"aliases": [
"bradley-bernstein:SS-LS_1553_R1",
"buenrostro-bernstein:SS-LS_1553_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:48:04.596045+00:00",
"file_format": "fastq",
"file_size": 9344,
"href": "/sequence-files/IGVFFI6506WNCM/@@download/IGVFFI6506WNCM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/9f677b37-45a3-481f-bb88-5bac8854fc6a/IGVFFI6506WNCM.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-1146_L2_SS-PKR-7_SS-V2-PLATE2-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0955TCWM/",
"accession": "IGVFFI0955TCWM",
"aliases": [
"bradley-bernstein:SS-LS_2319_R1",
"buenrostro-bernstein:SS-LS_2319_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:50:25.554258+00:00",
"file_format": "fastq",
"file_size": 596180118,
"href": "/sequence-files/IGVFFI0955TCWM/@@download/IGVFFI0955TCWM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/8ab1f798-be06-48d0-9fc1-d83247088a2f/IGVFFI0955TCWM.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-83_L1_SS-PKR-7_SS-V2-PLATE2-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3595THDP/",
"accession": "IGVFFI3595THDP",
"aliases": [
"bradley-bernstein:SS-LS_2319_R2",
"buenrostro-bernstein:SS-LS_2319_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:50:26.511341+00:00",
"file_format": "fastq",
"file_size": 1060596576,
"href": "/sequence-files/IGVFFI3595THDP/@@download/IGVFFI3595THDP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/dfbbd7bf-2af5-4485-8266-597e54f4a423/IGVFFI3595THDP.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-83_L1_SS-PKR-7_SS-V2-PLATE2-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1130RYAL/",
"accession": "IGVFFI1130RYAL",
"aliases": [
"bradley-bernstein:SS-LS_1457_R1",
"buenrostro-bernstein:SS-LS_1457_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:47:28.345419+00:00",
"file_format": "fastq",
"file_size": 8716,
"href": "/sequence-files/IGVFFI1130RYAL/@@download/IGVFFI1130RYAL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/3903dd7a-bae1-4d51-aa6c-1ec80188b4ef/IGVFFI1130RYAL.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-1146_L1_SS-PKR-7_SS-V2-PLATE2-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2824HWUQ/",
"accession": "IGVFFI2824HWUQ",
"aliases": [
"bradley-bernstein:SS-LS_1649_R2",
"buenrostro-bernstein:SS-LS_1649_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:48:46.389886+00:00",
"file_format": "fastq",
"file_size": 18329,
"href": "/sequence-files/IGVFFI2824HWUQ/@@download/IGVFFI2824HWUQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/5763c030-a695-4b17-8558-664230eb5cc2/IGVFFI2824HWUQ.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-1146_L3_SS-PKR-7_SS-V2-PLATE2-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9275YULT/",
"accession": "IGVFFI9275YULT",
"aliases": [
"bradley-bernstein:SS-LS_2511_R1",
"buenrostro-bernstein:SS-LS_2511_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:51:41.607840+00:00",
"file_format": "fastq",
"file_size": 597399269,
"href": "/sequence-files/IGVFFI9275YULT/@@download/IGVFFI9275YULT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/f7e96f88-03cd-4af6-8d5b-3b380145f6c6/IGVFFI9275YULT.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-83_L3_SS-PKR-7_SS-V2-PLATE2-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3574DKQS/",
"accession": "IGVFFI3574DKQS",
"aliases": [
"bradley-bernstein:SS-LS_1553_R2",
"buenrostro-bernstein:SS-LS_1553_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:48:05.665698+00:00",
"file_format": "fastq",
"file_size": 19549,
"href": "/sequence-files/IGVFFI3574DKQS/@@download/IGVFFI3574DKQS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/ce1b4bd9-7eb7-4c55-a2b9-85ca0800ec86/IGVFFI3574DKQS.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-1146_L2_SS-PKR-7_SS-V2-PLATE2-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6001NXCF/",
"accession": "IGVFFI6001NXCF",
"aliases": [
"bradley-bernstein:SS-LS_1745_R2",
"buenrostro-bernstein:SS-LS_1745_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:49:50.666430+00:00",
"file_format": "fastq",
"file_size": 19555,
"href": "/sequence-files/IGVFFI6001NXCF/@@download/IGVFFI6001NXCF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/cb86fb36-0ec3-4d99-b7a5-0ad376c70dfa/IGVFFI6001NXCF.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-1146_L4_SS-PKR-7_SS-V2-PLATE2-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9712CUJE/",
"accession": "IGVFFI9712CUJE",
"aliases": [
"bradley-bernstein:SS-LS_2415_R1",
"buenrostro-bernstein:SS-LS_2415_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:51:04.706127+00:00",
"file_format": "fastq",
"file_size": 598577334,
"href": "/sequence-files/IGVFFI9712CUJE/@@download/IGVFFI9712CUJE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/1df3cc16-be11-41b8-9adb-062304e26b11/IGVFFI9712CUJE.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-83_L2_SS-PKR-7_SS-V2-PLATE2-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8604CBGJ/",
"accession": "IGVFFI8604CBGJ",
"aliases": [
"bradley-bernstein:SS-LS_2607_R2",
"buenrostro-bernstein:SS-LS_2607_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:52:22.835431+00:00",
"file_format": "fastq",
"file_size": 1051031697,
"href": "/sequence-files/IGVFFI8604CBGJ/@@download/IGVFFI8604CBGJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/c2c62d01-4b1d-42a6-bad9-7f67b98c3275/IGVFFI8604CBGJ.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-83_L4_SS-PKR-7_SS-V2-PLATE2-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2734MPWM/",
"accession": "IGVFFI2734MPWM",
"aliases": [
"bradley-bernstein:SS-LS_2607_R1",
"buenrostro-bernstein:SS-LS_2607_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:52:21.928442+00:00",
"file_format": "fastq",
"file_size": 593443035,
"href": "/sequence-files/IGVFFI2734MPWM/@@download/IGVFFI2734MPWM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/2a009212-354f-4d9a-99f2-ab29d5a58649/IGVFFI2734MPWM.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-83_L4_SS-PKR-7_SS-V2-PLATE2-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9431LFUM/",
"accession": "IGVFFI9431LFUM",
"aliases": [
"bradley-bernstein:SS-LS_2415_R2",
"buenrostro-bernstein:SS-LS_2415_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:51:05.781471+00:00",
"file_format": "fastq",
"file_size": 1059882735,
"href": "/sequence-files/IGVFFI9431LFUM/@@download/IGVFFI9431LFUM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/9551dd59-8a7b-4298-8a65-dee9a86217cb/IGVFFI9431LFUM.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-83_L2_SS-PKR-7_SS-V2-PLATE2-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8527DQRD/",
"accession": "IGVFFI8527DQRD",
"aliases": [
"bradley-bernstein:SS-LS_2511_R2",
"buenrostro-bernstein:SS-LS_2511_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:51:42.588801+00:00",
"file_format": "fastq",
"file_size": 1055434316,
"href": "/sequence-files/IGVFFI8527DQRD/@@download/IGVFFI8527DQRD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/e8e9f850-1115-46f1-b0a6-6adfe7cda872/IGVFFI8527DQRD.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-83_L3_SS-PKR-7_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/IGVFDS2883IFIK/",
"accession": "IGVFDS2883IFIK",
"status": "released"
}
],
"release_timestamp": "2025-01-14T18:02:35.505525+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM1494VRXC/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1494VRXC",
"aliases": [
"bradley-bernstein:BioSam 4568_SS-PKR 7",
"buenrostro-bernstein:BioSam 4568_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 (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": "2024-02-12T21:47:28.345419+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "06fa2391-e375-41be-bcd6-4f4adb85c9ab"
}