{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0726CKKN/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0726CKKN",
"aliases": [
"bradley-bernstein:scATAC Lib 44",
"buenrostro-bernstein:scATAC Lib 44"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002764/",
"status": "released",
"term_name": "single-cell ATAC-seq"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0726CKKN](/measurement-sets/IGVFDS0726CKKN/) has sequence file(s): [IGVFFI2252OBVA](/sequence-files/IGVFFI2252OBVA/), [IGVFFI9479UJBX](/sequence-files/IGVFFI9479UJBX/), [IGVFFI8114OJUY](/sequence-files/IGVFFI8114OJUY/), [IGVFFI7272TKEH](/sequence-files/IGVFFI7272TKEH/), [IGVFFI0090SYWU](/sequence-files/IGVFFI0090SYWU/), [IGVFFI3122JWPM](/sequence-files/IGVFFI3122JWPM/), [IGVFFI5448BFBW](/sequence-files/IGVFFI5448BFBW/), [IGVFFI3218ARRR](/sequence-files/IGVFFI3218ARRR/), [IGVFFI3926QWGX](/sequence-files/IGVFFI3926QWGX/), [IGVFFI9674XTYU](/sequence-files/IGVFFI9674XTYU/), [IGVFFI0700SYLQ](/sequence-files/IGVFFI0700SYLQ/), [IGVFFI3130ZBUR](/sequence-files/IGVFFI3130ZBUR/), [IGVFFI0286XXOE](/sequence-files/IGVFFI0286XXOE/), [IGVFFI2962DQIK](/sequence-files/IGVFFI2962DQIK/), [IGVFFI0239ECJR](/sequence-files/IGVFFI0239ECJR/), [IGVFFI5365AXLH](/sequence-files/IGVFFI5365AXLH/) 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/IGVFDS0726CKKN/"
},
{
"category": "mismatched status",
"detail": "Released primary cell [IGVFSM8386QKSO](/primary-cells/IGVFSM8386QKSO/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/primary-cells/IGVFSM8386QKSO/"
}
],
"WARNING": [
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS0726CKKN](/measurement-sets/IGVFDS0726CKKN/) 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/IGVFDS0726CKKN/"
}
]
},
"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": "2024-02-12T21:12:38.816847+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/IGVFFI2252OBVA/",
"accession": "IGVFFI2252OBVA",
"aliases": [
"bradley-bernstein:SS-LS_1557_R1",
"buenrostro-bernstein:SS-LS_1557_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:26:17.336497+00:00",
"file_format": "fastq",
"file_size": 2700,
"href": "/sequence-files/IGVFFI2252OBVA/@@download/IGVFFI2252OBVA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/fc4fc83a-f656-4aef-93a3-cdaf764ec03a/IGVFFI2252OBVA.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-1150_L2_SS-PKR-8_SS-V1-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9479UJBX/",
"accession": "IGVFFI9479UJBX",
"aliases": [
"bradley-bernstein:SS-LS_2323_R1",
"buenrostro-bernstein:SS-LS_2323_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:28:28.639307+00:00",
"file_format": "fastq",
"file_size": 450737725,
"href": "/sequence-files/IGVFFI9479UJBX/@@download/IGVFFI9479UJBX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/13936b5d-7c07-4db9-8208-08a0c6acf0b3/IGVFFI9479UJBX.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-87_L1_SS-PKR-8_SS-V1-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8114OJUY/",
"accession": "IGVFFI8114OJUY",
"aliases": [
"bradley-bernstein:SS-LS_1653_R2",
"buenrostro-bernstein:SS-LS_1653_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:26:55.655847+00:00",
"file_format": "fastq",
"file_size": 3709,
"href": "/sequence-files/IGVFFI8114OJUY/@@download/IGVFFI8114OJUY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/56689a34-737a-469e-a8d9-f67df946f78a/IGVFFI8114OJUY.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-1150_L3_SS-PKR-8_SS-V1-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7272TKEH/",
"accession": "IGVFFI7272TKEH",
"aliases": [
"bradley-bernstein:SS-LS_1557_R2",
"buenrostro-bernstein:SS-LS_1557_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:26:18.467784+00:00",
"file_format": "fastq",
"file_size": 5057,
"href": "/sequence-files/IGVFFI7272TKEH/@@download/IGVFFI7272TKEH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/05d4e8e5-3028-4429-bb2c-96811c723674/IGVFFI7272TKEH.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-1150_L2_SS-PKR-8_SS-V1-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0090SYWU/",
"accession": "IGVFFI0090SYWU",
"aliases": [
"bradley-bernstein:SS-LS_1461_R2",
"buenrostro-bernstein:SS-LS_1461_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:25:43.135033+00:00",
"file_format": "fastq",
"file_size": 5020,
"href": "/sequence-files/IGVFFI0090SYWU/@@download/IGVFFI0090SYWU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/cc1bc584-dc34-4b16-8c1b-5dd705905e58/IGVFFI0090SYWU.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-1150_L1_SS-PKR-8_SS-V1-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3122JWPM/",
"accession": "IGVFFI3122JWPM",
"aliases": [
"bradley-bernstein:SS-LS_1749_R2",
"buenrostro-bernstein:SS-LS_1749_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:27:32.516135+00:00",
"file_format": "fastq",
"file_size": 5983,
"href": "/sequence-files/IGVFFI3122JWPM/@@download/IGVFFI3122JWPM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/6e4b0908-1591-4687-805a-f852432f77bb/IGVFFI3122JWPM.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-1150_L4_SS-PKR-8_SS-V1-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5448BFBW/",
"accession": "IGVFFI5448BFBW",
"aliases": [
"bradley-bernstein:SS-LS_2419_R2",
"buenrostro-bernstein:SS-LS_2419_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:29:08.847913+00:00",
"file_format": "fastq",
"file_size": 772933739,
"href": "/sequence-files/IGVFFI5448BFBW/@@download/IGVFFI5448BFBW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/8660ac50-de2a-4024-b39f-a315fa181f09/IGVFFI5448BFBW.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-87_L2_SS-PKR-8_SS-V1-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3218ARRR/",
"accession": "IGVFFI3218ARRR",
"aliases": [
"bradley-bernstein:SS-LS_1749_R1",
"buenrostro-bernstein:SS-LS_1749_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:27:31.398308+00:00",
"file_format": "fastq",
"file_size": 3142,
"href": "/sequence-files/IGVFFI3218ARRR/@@download/IGVFFI3218ARRR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/e677388e-eb33-4fbd-b917-155cf1fef717/IGVFFI3218ARRR.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-1150_L4_SS-PKR-8_SS-V1-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3926QWGX/",
"accession": "IGVFFI3926QWGX",
"aliases": [
"bradley-bernstein:SS-LS_1653_R1",
"buenrostro-bernstein:SS-LS_1653_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:26:54.612659+00:00",
"file_format": "fastq",
"file_size": 2103,
"href": "/sequence-files/IGVFFI3926QWGX/@@download/IGVFFI3926QWGX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/6b75141b-cd15-4126-a2e0-ff5bf53cf4dc/IGVFFI3926QWGX.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-1150_L3_SS-PKR-8_SS-V1-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9674XTYU/",
"accession": "IGVFFI9674XTYU",
"aliases": [
"bradley-bernstein:SS-LS_2419_R1",
"buenrostro-bernstein:SS-LS_2419_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:29:07.843859+00:00",
"file_format": "fastq",
"file_size": 452910598,
"href": "/sequence-files/IGVFFI9674XTYU/@@download/IGVFFI9674XTYU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/bb04737f-9eba-4c40-a0c7-201cce40c7d2/IGVFFI9674XTYU.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-87_L2_SS-PKR-8_SS-V1-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0700SYLQ/",
"accession": "IGVFFI0700SYLQ",
"aliases": [
"bradley-bernstein:SS-LS_2515_R1",
"buenrostro-bernstein:SS-LS_2515_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:29:41.111984+00:00",
"file_format": "fastq",
"file_size": 451278428,
"href": "/sequence-files/IGVFFI0700SYLQ/@@download/IGVFFI0700SYLQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/5e192f90-2eb1-4d5d-b766-345f2c6dfe1b/IGVFFI0700SYLQ.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-87_L3_SS-PKR-8_SS-V1-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3130ZBUR/",
"accession": "IGVFFI3130ZBUR",
"aliases": [
"bradley-bernstein:SS-LS_1461_R1",
"buenrostro-bernstein:SS-LS_1461_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:25:42.252190+00:00",
"file_format": "fastq",
"file_size": 2696,
"href": "/sequence-files/IGVFFI3130ZBUR/@@download/IGVFFI3130ZBUR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/065eacfe-eede-4bf6-8cae-82e7086b101e/IGVFFI3130ZBUR.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-1150_L1_SS-PKR-8_SS-V1-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0286XXOE/",
"accession": "IGVFFI0286XXOE",
"aliases": [
"bradley-bernstein:SS-LS_2323_R2",
"buenrostro-bernstein:SS-LS_2323_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:28:29.644432+00:00",
"file_format": "fastq",
"file_size": 770232849,
"href": "/sequence-files/IGVFFI0286XXOE/@@download/IGVFFI0286XXOE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/3953588c-7523-42b0-a96a-216aa322bb31/IGVFFI0286XXOE.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-87_L1_SS-PKR-8_SS-V1-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2962DQIK/",
"accession": "IGVFFI2962DQIK",
"aliases": [
"bradley-bernstein:SS-LS_2515_R2",
"buenrostro-bernstein:SS-LS_2515_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:29:43.193960+00:00",
"file_format": "fastq",
"file_size": 768665749,
"href": "/sequence-files/IGVFFI2962DQIK/@@download/IGVFFI2962DQIK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/4253145d-7119-40f9-abee-99a6e8f26945/IGVFFI2962DQIK.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-87_L3_SS-PKR-8_SS-V1-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0239ECJR/",
"accession": "IGVFFI0239ECJR",
"aliases": [
"bradley-bernstein:SS-LS_2611_R1",
"buenrostro-bernstein:SS-LS_2611_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:30:20.237005+00:00",
"file_format": "fastq",
"file_size": 446886405,
"href": "/sequence-files/IGVFFI0239ECJR/@@download/IGVFFI0239ECJR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/63ec990d-e968-4dca-be59-387dfc12aa0d/IGVFFI0239ECJR.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-87_L4_SS-PKR-8_SS-V1-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5365AXLH/",
"accession": "IGVFFI5365AXLH",
"aliases": [
"bradley-bernstein:SS-LS_2611_R2",
"buenrostro-bernstein:SS-LS_2611_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:30:21.359970+00:00",
"file_format": "fastq",
"file_size": 763082740,
"href": "/sequence-files/IGVFFI5365AXLH/@@download/IGVFFI5365AXLH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/bbf408d4-92d0-4726-83f5-d1313c2cfdde/IGVFFI5365AXLH.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-87_L4_SS-PKR-8_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/IGVFDS6493BIXB/",
"accession": "IGVFDS6493BIXB",
"status": "released"
}
],
"release_timestamp": "2025-01-14T17:53:02.344245+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM8386QKSO/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8386QKSO",
"aliases": [
"bradley-bernstein:BioSam 4564_SS-PKR 8",
"buenrostro-bernstein:BioSam 4564_SS-PKR 8"
],
"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 8), 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": "2024-02-12T21:25:42.252190+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "09de3959-f7eb-4da2-9277-552ad2b39740"
}