{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9263WCDZ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9263WCDZ",
"aliases": [
"bradley-bernstein:scRNA Lib 28",
"buenrostro-bernstein:scRNA Lib 28"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002631/",
"status": "released",
"term_name": "single-cell RNA sequencing assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released primary cell [IGVFSM9794GFPU](/primary-cells/IGVFSM9794GFPU/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/primary-cells/IGVFSM9794GFPU/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9263WCDZ](/measurement-sets/IGVFDS9263WCDZ/) has sequence file(s): [IGVFFI9501KPFA](/sequence-files/IGVFFI9501KPFA/), [IGVFFI1062HDUZ](/sequence-files/IGVFFI1062HDUZ/), [IGVFFI0367SUHH](/sequence-files/IGVFFI0367SUHH/), [IGVFFI6630OLMG](/sequence-files/IGVFFI6630OLMG/), [IGVFFI3220ZQVU](/sequence-files/IGVFFI3220ZQVU/), [IGVFFI3201TCOW](/sequence-files/IGVFFI3201TCOW/), [IGVFFI9930JOYI](/sequence-files/IGVFFI9930JOYI/), [IGVFFI8340YYPC](/sequence-files/IGVFFI8340YYPC/), [IGVFFI5922WGDT](/sequence-files/IGVFFI5922WGDT/), [IGVFFI4531IYID](/sequence-files/IGVFFI4531IYID/), [IGVFFI9135SBBX](/sequence-files/IGVFFI9135SBBX/), [IGVFFI4537AJOY](/sequence-files/IGVFFI4537AJOY/), [IGVFFI4754TXMU](/sequence-files/IGVFFI4754TXMU/), [IGVFFI0541OHXL](/sequence-files/IGVFFI0541OHXL/), [IGVFFI7139KSKS](/sequence-files/IGVFFI7139KSKS/), [IGVFFI2071UYOD](/sequence-files/IGVFFI2071UYOD/) 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/IGVFDS9263WCDZ/"
}
],
"WARNING": [
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS9263WCDZ](/measurement-sets/IGVFDS9263WCDZ/) has an `assay_term` of single-cell RNA sequencing assay 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/IGVFDS9263WCDZ/"
}
]
},
"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": "2024-02-12T21:12:57.130967+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO8549ATSE/",
"accession": "IGVFDO8549ATSE",
"aliases": [
"bradley-bernstein:Donor 1511",
"buenrostro-bernstein:Donor 1511"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI9501KPFA/",
"accession": "IGVFFI9501KPFA",
"aliases": [
"bradley-bernstein:SS-LS_1430_R2",
"buenrostro-bernstein:SS-LS_1430_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:36:05.767035+00:00",
"file_format": "fastq",
"file_size": 1555680635,
"href": "/sequence-files/IGVFFI9501KPFA/@@download/IGVFFI9501KPFA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/90fe4daf-6aa5-4d61-b142-77ae1b5330ca/IGVFFI9501KPFA.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-1119_L1_SS-PKR-5_SS-V2-PLATE2-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1062HDUZ/",
"accession": "IGVFFI1062HDUZ",
"aliases": [
"bradley-bernstein:SS-LS_1430_R1",
"buenrostro-bernstein:SS-LS_1430_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:36:04.841885+00:00",
"file_format": "fastq",
"file_size": 586802209,
"href": "/sequence-files/IGVFFI1062HDUZ/@@download/IGVFFI1062HDUZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/6c16160e-acf7-442d-814a-afee3e178e87/IGVFFI1062HDUZ.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-1119_L1_SS-PKR-5_SS-V2-PLATE2-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0367SUHH/",
"accession": "IGVFFI0367SUHH",
"aliases": [
"bradley-bernstein:SS-LS_2484_R1",
"buenrostro-bernstein:SS-LS_2484_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:40:05.583733+00:00",
"file_format": "fastq",
"file_size": 308648621,
"href": "/sequence-files/IGVFFI0367SUHH/@@download/IGVFFI0367SUHH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/bb287e27-64d6-4c86-beaa-4644cd3cd3cb/IGVFFI0367SUHH.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-56_L3_SS-PKR-5_SS-V2-PLATE2-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6630OLMG/",
"accession": "IGVFFI6630OLMG",
"aliases": [
"bradley-bernstein:SS-LS_2484_R2",
"buenrostro-bernstein:SS-LS_2484_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:40:06.706033+00:00",
"file_format": "fastq",
"file_size": 722883913,
"href": "/sequence-files/IGVFFI6630OLMG/@@download/IGVFFI6630OLMG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/6c223796-44a6-4a05-a0a7-1363a6830b00/IGVFFI6630OLMG.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-56_L3_SS-PKR-5_SS-V2-PLATE2-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3220ZQVU/",
"accession": "IGVFFI3220ZQVU",
"aliases": [
"bradley-bernstein:SS-LS_1526_R1",
"buenrostro-bernstein:SS-LS_1526_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:37:04.808899+00:00",
"file_format": "fastq",
"file_size": 596105301,
"href": "/sequence-files/IGVFFI3220ZQVU/@@download/IGVFFI3220ZQVU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/60ca5fc8-5180-41c4-96a6-d78c05272242/IGVFFI3220ZQVU.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-1119_L2_SS-PKR-5_SS-V2-PLATE2-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3201TCOW/",
"accession": "IGVFFI3201TCOW",
"aliases": [
"bradley-bernstein:SS-LS_1526_R2",
"buenrostro-bernstein:SS-LS_1526_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:37:05.803439+00:00",
"file_format": "fastq",
"file_size": 1578009970,
"href": "/sequence-files/IGVFFI3201TCOW/@@download/IGVFFI3201TCOW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/894a1ef0-b90c-4c1f-8e3b-6638c1bafd7a/IGVFFI3201TCOW.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-1119_L2_SS-PKR-5_SS-V2-PLATE2-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9930JOYI/",
"accession": "IGVFFI9930JOYI",
"aliases": [
"bradley-bernstein:SS-LS_1622_R1",
"buenrostro-bernstein:SS-LS_1622_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:37:42.375471+00:00",
"file_format": "fastq",
"file_size": 580588795,
"href": "/sequence-files/IGVFFI9930JOYI/@@download/IGVFFI9930JOYI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/22194091-6e36-4869-a151-83ac66c9ac8d/IGVFFI9930JOYI.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-1119_L3_SS-PKR-5_SS-V2-PLATE2-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8340YYPC/",
"accession": "IGVFFI8340YYPC",
"aliases": [
"bradley-bernstein:SS-LS_1622_R2",
"buenrostro-bernstein:SS-LS_1622_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:37:43.444976+00:00",
"file_format": "fastq",
"file_size": 1544538400,
"href": "/sequence-files/IGVFFI8340YYPC/@@download/IGVFFI8340YYPC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/d9e0ebaa-bdb2-4650-80ac-dada2c848e0d/IGVFFI8340YYPC.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-1119_L3_SS-PKR-5_SS-V2-PLATE2-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5922WGDT/",
"accession": "IGVFFI5922WGDT",
"aliases": [
"bradley-bernstein:SS-LS_1718_R1",
"buenrostro-bernstein:SS-LS_1718_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:38:18.731598+00:00",
"file_format": "fastq",
"file_size": 578986718,
"href": "/sequence-files/IGVFFI5922WGDT/@@download/IGVFFI5922WGDT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/645ae361-b713-4fe1-9e93-39442faba322/IGVFFI5922WGDT.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-1119_L4_SS-PKR-5_SS-V2-PLATE2-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4531IYID/",
"accession": "IGVFFI4531IYID",
"aliases": [
"bradley-bernstein:SS-LS_1718_R2",
"buenrostro-bernstein:SS-LS_1718_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:38:19.777258+00:00",
"file_format": "fastq",
"file_size": 1561515610,
"href": "/sequence-files/IGVFFI4531IYID/@@download/IGVFFI4531IYID.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/3de26dc5-8102-4b25-b744-e2747e958f6d/IGVFFI4531IYID.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-1119_L4_SS-PKR-5_SS-V2-PLATE2-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9135SBBX/",
"accession": "IGVFFI9135SBBX",
"aliases": [
"bradley-bernstein:SS-LS_2292_R2",
"buenrostro-bernstein:SS-LS_2292_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:38:54.604929+00:00",
"file_format": "fastq",
"file_size": 730704341,
"href": "/sequence-files/IGVFFI9135SBBX/@@download/IGVFFI9135SBBX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/bfd92dd8-b76b-410c-9c7e-53b0a9af5c81/IGVFFI9135SBBX.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-56_L1_SS-PKR-5_SS-V2-PLATE2-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4537AJOY/",
"accession": "IGVFFI4537AJOY",
"aliases": [
"bradley-bernstein:SS-LS_2292_R1",
"buenrostro-bernstein:SS-LS_2292_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:38:53.621857+00:00",
"file_format": "fastq",
"file_size": 308094745,
"href": "/sequence-files/IGVFFI4537AJOY/@@download/IGVFFI4537AJOY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/f9141ff2-fcae-415e-a9cd-206860ad4253/IGVFFI4537AJOY.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-56_L1_SS-PKR-5_SS-V2-PLATE2-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4754TXMU/",
"accession": "IGVFFI4754TXMU",
"aliases": [
"bradley-bernstein:SS-LS_2388_R1",
"buenrostro-bernstein:SS-LS_2388_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:39:30.131678+00:00",
"file_format": "fastq",
"file_size": 309935538,
"href": "/sequence-files/IGVFFI4754TXMU/@@download/IGVFFI4754TXMU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/6377e3ea-b3bf-4cb2-9287-b09be4310196/IGVFFI4754TXMU.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-56_L2_SS-PKR-5_SS-V2-PLATE2-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0541OHXL/",
"accession": "IGVFFI0541OHXL",
"aliases": [
"bradley-bernstein:SS-LS_2388_R2",
"buenrostro-bernstein:SS-LS_2388_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:39:31.097129+00:00",
"file_format": "fastq",
"file_size": 726286139,
"href": "/sequence-files/IGVFFI0541OHXL/@@download/IGVFFI0541OHXL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/8b8fa940-2bdf-4f4b-8cd3-ea0fdc44ddd7/IGVFFI0541OHXL.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-56_L2_SS-PKR-5_SS-V2-PLATE2-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7139KSKS/",
"accession": "IGVFFI7139KSKS",
"aliases": [
"bradley-bernstein:SS-LS_2580_R1",
"buenrostro-bernstein:SS-LS_2580_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:41:09.759985+00:00",
"file_format": "fastq",
"file_size": 303445364,
"href": "/sequence-files/IGVFFI7139KSKS/@@download/IGVFFI7139KSKS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/04e1e8f1-a438-4ea2-8276-20fa017d84cf/IGVFFI7139KSKS.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-56_L4_SS-PKR-5_SS-V2-PLATE2-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2071UYOD/",
"accession": "IGVFFI2071UYOD",
"aliases": [
"bradley-bernstein:SS-LS_2580_R2",
"buenrostro-bernstein:SS-LS_2580_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:41:11.272551+00:00",
"file_format": "fastq",
"file_size": 712576625,
"href": "/sequence-files/IGVFFI2071UYOD/@@download/IGVFFI2071UYOD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/d8e237d3-4bff-4d85-820d-a7e3ddd0839e/IGVFFI2071UYOD.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-56_L4_SS-PKR-5_SS-V2-PLATE2-1st-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/IGVFDS8367BZNA/",
"accession": "IGVFDS8367BZNA",
"status": "released"
}
],
"release_timestamp": "2025-01-14T19:29:56.993597+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM9794GFPU/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9794GFPU",
"aliases": [
"bradley-bernstein:BioSam 4566_SS-PKR 5",
"buenrostro-bernstein:BioSam 4566_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 (49 years)",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2024-02-12T21:36:04.841885+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "f40f72dd-52a8-43a2-8f20-0d04a90472c0"
}