{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7101YHDI/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7101YHDI",
"aliases": [
"bradley-bernstein:scATAC Lib 31",
"buenrostro-bernstein:scATAC Lib 31"
],
"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 [IGVFSM4055GPWI](/primary-cells/IGVFSM4055GPWI/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/primary-cells/IGVFSM4055GPWI/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7101YHDI](/measurement-sets/IGVFDS7101YHDI/) has sequence file(s): [IGVFFI5769LQRV](/sequence-files/IGVFFI5769LQRV/), [IGVFFI4254DMVD](/sequence-files/IGVFFI4254DMVD/), [IGVFFI9392CCHC](/sequence-files/IGVFFI9392CCHC/), [IGVFFI0364JRSK](/sequence-files/IGVFFI0364JRSK/), [IGVFFI8443FCCE](/sequence-files/IGVFFI8443FCCE/), [IGVFFI3968DFBW](/sequence-files/IGVFFI3968DFBW/), [IGVFFI8883WARZ](/sequence-files/IGVFFI8883WARZ/), [IGVFFI6231VTFN](/sequence-files/IGVFFI6231VTFN/), [IGVFFI9274JICV](/sequence-files/IGVFFI9274JICV/), [IGVFFI2185EZQY](/sequence-files/IGVFFI2185EZQY/), [IGVFFI4326WXLR](/sequence-files/IGVFFI4326WXLR/), [IGVFFI8424QNYH](/sequence-files/IGVFFI8424QNYH/), [IGVFFI4516SCBW](/sequence-files/IGVFFI4516SCBW/), [IGVFFI0844GTKN](/sequence-files/IGVFFI0844GTKN/), [IGVFFI8430CNFB](/sequence-files/IGVFFI8430CNFB/), [IGVFFI5290PCXU](/sequence-files/IGVFFI5290PCXU/) 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/IGVFDS7101YHDI/"
}
],
"WARNING": [
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS7101YHDI](/measurement-sets/IGVFDS7101YHDI/) 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/IGVFDS7101YHDI/"
}
]
},
"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": "2024-02-12T21:12:26.081229+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/IGVFFI5769LQRV/",
"accession": "IGVFFI5769LQRV",
"aliases": [
"bradley-bernstein:SS-LS_1435_R1",
"buenrostro-bernstein:SS-LS_1435_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:23:41.710243+00:00",
"file_format": "fastq",
"file_size": 45152,
"href": "/sequence-files/IGVFFI5769LQRV/@@download/IGVFFI5769LQRV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/f49e2c0f-a99a-4bd7-840f-dd1d6e348506/IGVFFI5769LQRV.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-1124_L1_SS-PKR-6_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4254DMVD/",
"accession": "IGVFFI4254DMVD",
"aliases": [
"bradley-bernstein:SS-LS_1435_R2",
"buenrostro-bernstein:SS-LS_1435_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:23:42.708121+00:00",
"file_format": "fastq",
"file_size": 96652,
"href": "/sequence-files/IGVFFI4254DMVD/@@download/IGVFFI4254DMVD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/5e7a5d82-1ea2-4842-a9f1-93883025f5e0/IGVFFI4254DMVD.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-1124_L1_SS-PKR-6_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9392CCHC/",
"accession": "IGVFFI9392CCHC",
"aliases": [
"bradley-bernstein:SS-LS_1531_R1",
"buenrostro-bernstein:SS-LS_1531_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:28:06.110183+00:00",
"file_format": "fastq",
"file_size": 46188,
"href": "/sequence-files/IGVFFI9392CCHC/@@download/IGVFFI9392CCHC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/1c3fe8ed-7556-45c6-9707-43449798fa8f/IGVFFI9392CCHC.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-1124_L2_SS-PKR-6_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0364JRSK/",
"accession": "IGVFFI0364JRSK",
"aliases": [
"bradley-bernstein:SS-LS_1531_R2",
"buenrostro-bernstein:SS-LS_1531_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:28:07.122665+00:00",
"file_format": "fastq",
"file_size": 99156,
"href": "/sequence-files/IGVFFI0364JRSK/@@download/IGVFFI0364JRSK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/fd3b40bc-5f0a-4e84-9cd7-d4044d8a7136/IGVFFI0364JRSK.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-1124_L2_SS-PKR-6_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8443FCCE/",
"accession": "IGVFFI8443FCCE",
"aliases": [
"bradley-bernstein:SS-LS_2489_R1",
"buenrostro-bernstein:SS-LS_2489_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:24:16.568965+00:00",
"file_format": "fastq",
"file_size": 531380081,
"href": "/sequence-files/IGVFFI8443FCCE/@@download/IGVFFI8443FCCE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/db5c2d43-1647-4f60-82b9-d240b0a15c38/IGVFFI8443FCCE.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-61_L3_SS-PKR-6_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3968DFBW/",
"accession": "IGVFFI3968DFBW",
"aliases": [
"bradley-bernstein:SS-LS_2585_R1",
"buenrostro-bernstein:SS-LS_2585_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:24:53.468701+00:00",
"file_format": "fastq",
"file_size": 528191908,
"href": "/sequence-files/IGVFFI3968DFBW/@@download/IGVFFI3968DFBW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/76aec3e7-2e1d-4087-8db3-d259cfa359ba/IGVFFI3968DFBW.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-61_L4_SS-PKR-6_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8883WARZ/",
"accession": "IGVFFI8883WARZ",
"aliases": [
"bradley-bernstein:SS-LS_2585_R2",
"buenrostro-bernstein:SS-LS_2585_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:24:54.310362+00:00",
"file_format": "fastq",
"file_size": 903647509,
"href": "/sequence-files/IGVFFI8883WARZ/@@download/IGVFFI8883WARZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/5a695524-dbec-4b3f-8579-d28e2ceae1b8/IGVFFI8883WARZ.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-61_L4_SS-PKR-6_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6231VTFN/",
"accession": "IGVFFI6231VTFN",
"aliases": [
"bradley-bernstein:SS-LS_2489_R2",
"buenrostro-bernstein:SS-LS_2489_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:24:17.527664+00:00",
"file_format": "fastq",
"file_size": 906724222,
"href": "/sequence-files/IGVFFI6231VTFN/@@download/IGVFFI6231VTFN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/a5cc37b0-b3a9-4e4b-b7b6-edd9c97c88cf/IGVFFI6231VTFN.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-61_L3_SS-PKR-6_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9274JICV/",
"accession": "IGVFFI9274JICV",
"aliases": [
"bradley-bernstein:SS-LS_1627_R2",
"buenrostro-bernstein:SS-LS_1627_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:36:28.691794+00:00",
"file_format": "fastq",
"file_size": 94537,
"href": "/sequence-files/IGVFFI9274JICV/@@download/IGVFFI9274JICV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/40f1e7e2-5ee1-4093-b52c-37d4c3bdf82b/IGVFFI9274JICV.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-1124_L3_SS-PKR-6_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2185EZQY/",
"accession": "IGVFFI2185EZQY",
"aliases": [
"bradley-bernstein:SS-LS_1627_R1",
"buenrostro-bernstein:SS-LS_1627_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:36:27.816686+00:00",
"file_format": "fastq",
"file_size": 44232,
"href": "/sequence-files/IGVFFI2185EZQY/@@download/IGVFFI2185EZQY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/4b15a6ea-5d28-49c2-89b5-a7eb75f4a0c6/IGVFFI2185EZQY.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-1124_L3_SS-PKR-6_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4326WXLR/",
"accession": "IGVFFI4326WXLR",
"aliases": [
"bradley-bernstein:SS-LS_1723_R2",
"buenrostro-bernstein:SS-LS_1723_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:40:54.001881+00:00",
"file_format": "fastq",
"file_size": 100109,
"href": "/sequence-files/IGVFFI4326WXLR/@@download/IGVFFI4326WXLR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/4c8a15d2-2219-4c74-a666-8b24dcc7a257/IGVFFI4326WXLR.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-1124_L4_SS-PKR-6_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8424QNYH/",
"accession": "IGVFFI8424QNYH",
"aliases": [
"bradley-bernstein:SS-LS_1723_R1",
"buenrostro-bernstein:SS-LS_1723_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:40:52.695803+00:00",
"file_format": "fastq",
"file_size": 46874,
"href": "/sequence-files/IGVFFI8424QNYH/@@download/IGVFFI8424QNYH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/694eb2b1-81f3-4a15-8f4b-a98e61c19c90/IGVFFI8424QNYH.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-1124_L4_SS-PKR-6_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4516SCBW/",
"accession": "IGVFFI4516SCBW",
"aliases": [
"bradley-bernstein:SS-LS_2297_R1",
"buenrostro-bernstein:SS-LS_2297_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:49:34.790032+00:00",
"file_format": "fastq",
"file_size": 530638700,
"href": "/sequence-files/IGVFFI4516SCBW/@@download/IGVFFI4516SCBW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/baf2cd3e-2081-4245-af97-eca67292d02e/IGVFFI4516SCBW.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-61_L1_SS-PKR-6_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0844GTKN/",
"accession": "IGVFFI0844GTKN",
"aliases": [
"bradley-bernstein:SS-LS_2297_R2",
"buenrostro-bernstein:SS-LS_2297_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:49:35.686286+00:00",
"file_format": "fastq",
"file_size": 907688106,
"href": "/sequence-files/IGVFFI0844GTKN/@@download/IGVFFI0844GTKN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/83814d68-6e55-4827-b468-0208dea2989d/IGVFFI0844GTKN.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-61_L1_SS-PKR-6_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8430CNFB/",
"accession": "IGVFFI8430CNFB",
"aliases": [
"bradley-bernstein:SS-LS_2393_R1",
"buenrostro-bernstein:SS-LS_2393_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:52:53.712221+00:00",
"file_format": "fastq",
"file_size": 534528847,
"href": "/sequence-files/IGVFFI8430CNFB/@@download/IGVFFI8430CNFB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/ab9e987c-994e-4f3c-a46d-7968bfcd454c/IGVFFI8430CNFB.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-61_L2_SS-PKR-6_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5290PCXU/",
"accession": "IGVFFI5290PCXU",
"aliases": [
"bradley-bernstein:SS-LS_2393_R2",
"buenrostro-bernstein:SS-LS_2393_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:52:54.692210+00:00",
"file_format": "fastq",
"file_size": 914009673,
"href": "/sequence-files/IGVFFI5290PCXU/@@download/IGVFFI5290PCXU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/60a2c787-b7f1-45e8-93b0-c5a28a55475d/IGVFFI5290PCXU.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-61_L2_SS-PKR-6_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/IGVFDS5863OHYL/",
"accession": "IGVFDS5863OHYL",
"status": "released"
}
],
"release_timestamp": "2025-01-14T19:42:52.246514+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM4055GPWI/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4055GPWI",
"aliases": [
"bradley-bernstein:BioSam 4563_SS-PKR 6",
"buenrostro-bernstein:BioSam 4563_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), 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": "2024-02-12T21:23:41.710243+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "fa450acd-87b9-48d9-8307-c2fc9a856c18"
}