{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5237LXYL/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5237LXYL",
"aliases": [
"bradley-bernstein:scRNA Lib 45",
"buenrostro-bernstein:scRNA Lib 45"
],
"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 [IGVFSM8124KBOC](/primary-cells/IGVFSM8124KBOC/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/primary-cells/IGVFSM8124KBOC/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5237LXYL](/measurement-sets/IGVFDS5237LXYL/) has sequence file(s): [IGVFFI3208NPHC](/sequence-files/IGVFFI3208NPHC/), [IGVFFI6308LATE](/sequence-files/IGVFFI6308LATE/), [IGVFFI3316BLYO](/sequence-files/IGVFFI3316BLYO/), [IGVFFI1899NTPL](/sequence-files/IGVFFI1899NTPL/), [IGVFFI1466RJGP](/sequence-files/IGVFFI1466RJGP/), [IGVFFI6105TGWW](/sequence-files/IGVFFI6105TGWW/), [IGVFFI6086TZYI](/sequence-files/IGVFFI6086TZYI/), [IGVFFI1994FZIR](/sequence-files/IGVFFI1994FZIR/), [IGVFFI1078HMII](/sequence-files/IGVFFI1078HMII/), [IGVFFI4344OWDS](/sequence-files/IGVFFI4344OWDS/), [IGVFFI7117SZNG](/sequence-files/IGVFFI7117SZNG/), [IGVFFI3397CVAJ](/sequence-files/IGVFFI3397CVAJ/), [IGVFFI0225TBCI](/sequence-files/IGVFFI0225TBCI/), [IGVFFI6881DROW](/sequence-files/IGVFFI6881DROW/), [IGVFFI0764YLOD](/sequence-files/IGVFFI0764YLOD/), [IGVFFI7271MEKR](/sequence-files/IGVFFI7271MEKR/) 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/IGVFDS5237LXYL/"
}
],
"WARNING": [
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS5237LXYL](/measurement-sets/IGVFDS5237LXYL/) 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/IGVFDS5237LXYL/"
}
]
},
"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": "2024-02-12T21:12:49.207233+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO2457AMDL/",
"accession": "IGVFDO2457AMDL",
"aliases": [
"bradley-bernstein:Donor 1509",
"buenrostro-bernstein:Donor 1509"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI3208NPHC/",
"accession": "IGVFFI3208NPHC",
"aliases": [
"bradley-bernstein:SS-LS_1656_R1",
"buenrostro-bernstein:SS-LS_1656_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:32:36.068715+00:00",
"file_format": "fastq",
"file_size": 997749972,
"href": "/sequence-files/IGVFFI3208NPHC/@@download/IGVFFI3208NPHC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/521c43f9-84e0-449b-a0d8-0db84e551155/IGVFFI3208NPHC.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-1153_L3_SS-PKR-8_SS-V1-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6308LATE/",
"accession": "IGVFFI6308LATE",
"aliases": [
"bradley-bernstein:SS-LS_2326_R1",
"buenrostro-bernstein:SS-LS_2326_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:33:52.945042+00:00",
"file_format": "fastq",
"file_size": 527960688,
"href": "/sequence-files/IGVFFI6308LATE/@@download/IGVFFI6308LATE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/3b7c799b-b867-4251-9b56-e105e88a585d/IGVFFI6308LATE.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-90_L1_SS-PKR-8_SS-V1-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3316BLYO/",
"accession": "IGVFFI3316BLYO",
"aliases": [
"bradley-bernstein:SS-LS_2326_R2",
"buenrostro-bernstein:SS-LS_2326_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:33:54.060911+00:00",
"file_format": "fastq",
"file_size": 1123543414,
"href": "/sequence-files/IGVFFI3316BLYO/@@download/IGVFFI3316BLYO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/dcfb18ea-84be-408d-958f-8ac3f217f300/IGVFFI3316BLYO.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-90_L1_SS-PKR-8_SS-V1-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1899NTPL/",
"accession": "IGVFFI1899NTPL",
"aliases": [
"bradley-bernstein:SS-LS_1464_R1",
"buenrostro-bernstein:SS-LS_1464_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:31:00.206662+00:00",
"file_format": "fastq",
"file_size": 999808764,
"href": "/sequence-files/IGVFFI1899NTPL/@@download/IGVFFI1899NTPL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/1fa6f0b9-fb7a-4677-a4da-bf4ea1c9df60/IGVFFI1899NTPL.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-1153_L1_SS-PKR-8_SS-V1-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1466RJGP/",
"accession": "IGVFFI1466RJGP",
"aliases": [
"bradley-bernstein:SS-LS_1464_R2",
"buenrostro-bernstein:SS-LS_1464_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:31:01.266786+00:00",
"file_format": "fastq",
"file_size": 2363692949,
"href": "/sequence-files/IGVFFI1466RJGP/@@download/IGVFFI1466RJGP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/09e98321-8f3d-4c2a-a94d-35e678ed8163/IGVFFI1466RJGP.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-1153_L1_SS-PKR-8_SS-V1-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6105TGWW/",
"accession": "IGVFFI6105TGWW",
"aliases": [
"bradley-bernstein:SS-LS_1560_R1",
"buenrostro-bernstein:SS-LS_1560_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:31:35.716820+00:00",
"file_format": "fastq",
"file_size": 1013088335,
"href": "/sequence-files/IGVFFI6105TGWW/@@download/IGVFFI6105TGWW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/068faa67-6933-4213-b309-b2ec8100bdd9/IGVFFI6105TGWW.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-1153_L2_SS-PKR-8_SS-V1-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6086TZYI/",
"accession": "IGVFFI6086TZYI",
"aliases": [
"bradley-bernstein:SS-LS_1560_R2",
"buenrostro-bernstein:SS-LS_1560_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:31:36.818678+00:00",
"file_format": "fastq",
"file_size": 2397596341,
"href": "/sequence-files/IGVFFI6086TZYI/@@download/IGVFFI6086TZYI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/63035cd6-2415-4e03-91d3-48b87fc814f3/IGVFFI6086TZYI.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-1153_L2_SS-PKR-8_SS-V1-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1994FZIR/",
"accession": "IGVFFI1994FZIR",
"aliases": [
"bradley-bernstein:SS-LS_1656_R2",
"buenrostro-bernstein:SS-LS_1656_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:32:37.063292+00:00",
"file_format": "fastq",
"file_size": 2353215838,
"href": "/sequence-files/IGVFFI1994FZIR/@@download/IGVFFI1994FZIR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/4cbb00bd-2e48-4525-953f-81ef256e3a76/IGVFFI1994FZIR.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-1153_L3_SS-PKR-8_SS-V1-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1078HMII/",
"accession": "IGVFFI1078HMII",
"aliases": [
"bradley-bernstein:SS-LS_2614_R1",
"buenrostro-bernstein:SS-LS_2614_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:35:42.983475+00:00",
"file_format": "fastq",
"file_size": 518095860,
"href": "/sequence-files/IGVFFI1078HMII/@@download/IGVFFI1078HMII.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/8c12fca0-41e7-4710-83c2-e8c2a90fba5f/IGVFFI1078HMII.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-90_L4_SS-PKR-8_SS-V1-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4344OWDS/",
"accession": "IGVFFI4344OWDS",
"aliases": [
"bradley-bernstein:SS-LS_2614_R2",
"buenrostro-bernstein:SS-LS_2614_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:35:43.911173+00:00",
"file_format": "fastq",
"file_size": 1106668617,
"href": "/sequence-files/IGVFFI4344OWDS/@@download/IGVFFI4344OWDS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/63cd585c-2bf1-4e8c-8efc-019ac8742cac/IGVFFI4344OWDS.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-90_L4_SS-PKR-8_SS-V1-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7117SZNG/",
"accession": "IGVFFI7117SZNG",
"aliases": [
"bradley-bernstein:SS-LS_2422_R1",
"buenrostro-bernstein:SS-LS_2422_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:34:31.798146+00:00",
"file_format": "fastq",
"file_size": 528960083,
"href": "/sequence-files/IGVFFI7117SZNG/@@download/IGVFFI7117SZNG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/b77b344b-f06a-471a-9f25-abfc457ef6f9/IGVFFI7117SZNG.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-90_L2_SS-PKR-8_SS-V1-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3397CVAJ/",
"accession": "IGVFFI3397CVAJ",
"aliases": [
"bradley-bernstein:SS-LS_1752_R1",
"buenrostro-bernstein:SS-LS_1752_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:33:11.856885+00:00",
"file_format": "fastq",
"file_size": 1012728904,
"href": "/sequence-files/IGVFFI3397CVAJ/@@download/IGVFFI3397CVAJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/39ea56af-79ce-45ea-82e5-40c236ac5faf/IGVFFI3397CVAJ.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-1153_L4_SS-PKR-8_SS-V1-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0225TBCI/",
"accession": "IGVFFI0225TBCI",
"aliases": [
"bradley-bernstein:SS-LS_1752_R2",
"buenrostro-bernstein:SS-LS_1752_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:33:12.869000+00:00",
"file_format": "fastq",
"file_size": 2396617233,
"href": "/sequence-files/IGVFFI0225TBCI/@@download/IGVFFI0225TBCI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/e14d923e-92b9-4317-b821-8e931ea7d77c/IGVFFI0225TBCI.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-1153_L4_SS-PKR-8_SS-V1-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6881DROW/",
"accession": "IGVFFI6881DROW",
"aliases": [
"bradley-bernstein:SS-LS_2422_R2",
"buenrostro-bernstein:SS-LS_2422_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:34:32.856278+00:00",
"file_format": "fastq",
"file_size": 1125941790,
"href": "/sequence-files/IGVFFI6881DROW/@@download/IGVFFI6881DROW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/e0ae8a79-07fc-4f2f-a8f8-7a5e4f56492e/IGVFFI6881DROW.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-90_L2_SS-PKR-8_SS-V1-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0764YLOD/",
"accession": "IGVFFI0764YLOD",
"aliases": [
"bradley-bernstein:SS-LS_2518_R1",
"buenrostro-bernstein:SS-LS_2518_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:35:06.705463+00:00",
"file_format": "fastq",
"file_size": 526320076,
"href": "/sequence-files/IGVFFI0764YLOD/@@download/IGVFFI0764YLOD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/de75fee2-d010-4830-b2bd-e8ac38ca7f6b/IGVFFI0764YLOD.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-90_L3_SS-PKR-8_SS-V1-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7271MEKR/",
"accession": "IGVFFI7271MEKR",
"aliases": [
"bradley-bernstein:SS-LS_2518_R2",
"buenrostro-bernstein:SS-LS_2518_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:35:07.645481+00:00",
"file_format": "fastq",
"file_size": 1118596034,
"href": "/sequence-files/IGVFFI7271MEKR/@@download/IGVFFI7271MEKR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/be2c5d28-7196-46b4-87ed-8c61f35673bf/IGVFFI7271MEKR.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-90_L3_SS-PKR-8_SS-V1-3rd-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/IGVFDS1519SERB/",
"accession": "IGVFDS1519SERB",
"status": "released"
}
],
"release_timestamp": "2025-01-14T19:41:34.869185+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM8124KBOC/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8124KBOC",
"aliases": [
"bradley-bernstein:BioSam 4565_SS-PKR 8",
"buenrostro-bernstein:BioSam 4565_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), male, Homo sapiens (29 years)",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2024-02-12T21:31:00.206662+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "3312736c-e6e1-437d-b214-13467e1e8b69"
}