{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5668ABKL/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5668ABKL",
"aliases": [
"bradley-bernstein:scRNA Lib 43",
"buenrostro-bernstein:scRNA Lib 43"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002631/",
"status": "released",
"term_name": "single-cell RNA sequencing assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5668ABKL](/measurement-sets/IGVFDS5668ABKL/) has sequence file(s): [IGVFFI1883LDEV](/sequence-files/IGVFFI1883LDEV/), [IGVFFI1113DVFE](/sequence-files/IGVFFI1113DVFE/), [IGVFFI6763XKMZ](/sequence-files/IGVFFI6763XKMZ/), [IGVFFI9319IYFO](/sequence-files/IGVFFI9319IYFO/), [IGVFFI0544CQBV](/sequence-files/IGVFFI0544CQBV/), [IGVFFI1639RGVH](/sequence-files/IGVFFI1639RGVH/), [IGVFFI3535IPBX](/sequence-files/IGVFFI3535IPBX/), [IGVFFI7695COZJ](/sequence-files/IGVFFI7695COZJ/), [IGVFFI3941MFGJ](/sequence-files/IGVFFI3941MFGJ/), [IGVFFI1388WNFS](/sequence-files/IGVFFI1388WNFS/), [IGVFFI8152QVAZ](/sequence-files/IGVFFI8152QVAZ/), [IGVFFI2508YYAX](/sequence-files/IGVFFI2508YYAX/), [IGVFFI8648AKRN](/sequence-files/IGVFFI8648AKRN/), [IGVFFI2373YPAG](/sequence-files/IGVFFI2373YPAG/), [IGVFFI4646TXRE](/sequence-files/IGVFFI4646TXRE/), [IGVFFI9887GGFU](/sequence-files/IGVFFI9887GGFU/) 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/IGVFDS5668ABKL/"
},
{
"category": "mismatched status",
"detail": "Released primary cell [IGVFSM1054BSTI](/primary-cells/IGVFSM1054BSTI/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/primary-cells/IGVFSM1054BSTI/"
}
],
"WARNING": [
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS5668ABKL](/measurement-sets/IGVFDS5668ABKL/) 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/IGVFDS5668ABKL/"
}
]
},
"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": "2024-02-12T21:12:28.900298+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/IGVFFI1883LDEV/",
"accession": "IGVFFI1883LDEV",
"aliases": [
"bradley-bernstein:SS-LS_2610_R2",
"buenrostro-bernstein:SS-LS_2610_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:25:05.367481+00:00",
"file_format": "fastq",
"file_size": 1303300557,
"href": "/sequence-files/IGVFFI1883LDEV/@@download/IGVFFI1883LDEV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/b5a92adf-80e4-4303-88e4-6338b3786b4f/IGVFFI1883LDEV.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-86_L4_SS-PKR-8_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1113DVFE/",
"accession": "IGVFFI1113DVFE",
"aliases": [
"bradley-bernstein:SS-LS_1460_R1",
"buenrostro-bernstein:SS-LS_1460_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:23:51.968197+00:00",
"file_format": "fastq",
"file_size": 1190837931,
"href": "/sequence-files/IGVFFI1113DVFE/@@download/IGVFFI1113DVFE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/7b949c36-ef62-4c29-a805-b124524bd8de/IGVFFI1113DVFE.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-1149_L1_SS-PKR-8_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6763XKMZ/",
"accession": "IGVFFI6763XKMZ",
"aliases": [
"bradley-bernstein:SS-LS_1460_R2",
"buenrostro-bernstein:SS-LS_1460_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:23:52.953793+00:00",
"file_format": "fastq",
"file_size": 2809565136,
"href": "/sequence-files/IGVFFI6763XKMZ/@@download/IGVFFI6763XKMZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/948b2f16-37b2-4dcc-9972-d6db2e142b59/IGVFFI6763XKMZ.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-1149_L1_SS-PKR-8_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9319IYFO/",
"accession": "IGVFFI9319IYFO",
"aliases": [
"bradley-bernstein:SS-LS_2514_R2",
"buenrostro-bernstein:SS-LS_2514_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:24:29.701622+00:00",
"file_format": "fastq",
"file_size": 1318483947,
"href": "/sequence-files/IGVFFI9319IYFO/@@download/IGVFFI9319IYFO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/c8ee15d3-7dfe-42de-a8d4-88ff029b4db1/IGVFFI9319IYFO.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-86_L3_SS-PKR-8_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0544CQBV/",
"accession": "IGVFFI0544CQBV",
"aliases": [
"bradley-bernstein:SS-LS_2610_R1",
"buenrostro-bernstein:SS-LS_2610_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:25:04.427397+00:00",
"file_format": "fastq",
"file_size": 614174836,
"href": "/sequence-files/IGVFFI0544CQBV/@@download/IGVFFI0544CQBV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/8a68917e-b460-4c11-8769-5c0b9a977be2/IGVFFI0544CQBV.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-86_L4_SS-PKR-8_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1639RGVH/",
"accession": "IGVFFI1639RGVH",
"aliases": [
"bradley-bernstein:SS-LS_2514_R1",
"buenrostro-bernstein:SS-LS_2514_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:24:28.781881+00:00",
"file_format": "fastq",
"file_size": 624414781,
"href": "/sequence-files/IGVFFI1639RGVH/@@download/IGVFFI1639RGVH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/97bcf70c-8439-4313-943e-a6031550d077/IGVFFI1639RGVH.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-86_L3_SS-PKR-8_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3535IPBX/",
"accession": "IGVFFI3535IPBX",
"aliases": [
"bradley-bernstein:SS-LS_1556_R1",
"buenrostro-bernstein:SS-LS_1556_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:32:09.400786+00:00",
"file_format": "fastq",
"file_size": 1206907857,
"href": "/sequence-files/IGVFFI3535IPBX/@@download/IGVFFI3535IPBX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/39fe9717-e768-44b4-a430-6fd224f1bae5/IGVFFI3535IPBX.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-1149_L2_SS-PKR-8_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7695COZJ/",
"accession": "IGVFFI7695COZJ",
"aliases": [
"bradley-bernstein:SS-LS_1556_R2",
"buenrostro-bernstein:SS-LS_1556_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:32:10.277546+00:00",
"file_format": "fastq",
"file_size": 2851069385,
"href": "/sequence-files/IGVFFI7695COZJ/@@download/IGVFFI7695COZJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/f98f6d80-29d4-458f-b792-3a3117659836/IGVFFI7695COZJ.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-1149_L2_SS-PKR-8_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3941MFGJ/",
"accession": "IGVFFI3941MFGJ",
"aliases": [
"bradley-bernstein:SS-LS_1652_R1",
"buenrostro-bernstein:SS-LS_1652_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:36:38.630085+00:00",
"file_format": "fastq",
"file_size": 1188865164,
"href": "/sequence-files/IGVFFI3941MFGJ/@@download/IGVFFI3941MFGJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/a59266f8-ecde-4c0b-862e-9591f4f9f2fc/IGVFFI3941MFGJ.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-1149_L3_SS-PKR-8_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1388WNFS/",
"accession": "IGVFFI1388WNFS",
"aliases": [
"bradley-bernstein:SS-LS_1652_R2",
"buenrostro-bernstein:SS-LS_1652_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:36:39.571885+00:00",
"file_format": "fastq",
"file_size": 2798219495,
"href": "/sequence-files/IGVFFI1388WNFS/@@download/IGVFFI1388WNFS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/a9a94c9d-de2a-4e6b-ad87-0b4b4156add5/IGVFFI1388WNFS.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-1149_L3_SS-PKR-8_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8152QVAZ/",
"accession": "IGVFFI8152QVAZ",
"aliases": [
"bradley-bernstein:SS-LS_1748_R2",
"buenrostro-bernstein:SS-LS_1748_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:45:05.809456+00:00",
"file_format": "fastq",
"file_size": 2849604200,
"href": "/sequence-files/IGVFFI8152QVAZ/@@download/IGVFFI8152QVAZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/0badec04-1162-45a7-957b-9728b31f5bc1/IGVFFI8152QVAZ.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-1149_L4_SS-PKR-8_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2508YYAX/",
"accession": "IGVFFI2508YYAX",
"aliases": [
"bradley-bernstein:SS-LS_2322_R1",
"buenrostro-bernstein:SS-LS_2322_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:49:44.540003+00:00",
"file_format": "fastq",
"file_size": 626861979,
"href": "/sequence-files/IGVFFI2508YYAX/@@download/IGVFFI2508YYAX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/b72fdc41-9773-4f00-be64-930ecabeb131/IGVFFI2508YYAX.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-86_L1_SS-PKR-8_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8648AKRN/",
"accession": "IGVFFI8648AKRN",
"aliases": [
"bradley-bernstein:SS-LS_1748_R1",
"buenrostro-bernstein:SS-LS_1748_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:45:04.677521+00:00",
"file_format": "fastq",
"file_size": 1206860952,
"href": "/sequence-files/IGVFFI8648AKRN/@@download/IGVFFI8648AKRN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/f8478864-ee60-4589-90f4-21c688dd6bbe/IGVFFI8648AKRN.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-1149_L4_SS-PKR-8_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2373YPAG/",
"accession": "IGVFFI2373YPAG",
"aliases": [
"bradley-bernstein:SS-LS_2322_R2",
"buenrostro-bernstein:SS-LS_2322_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:49:45.683343+00:00",
"file_format": "fastq",
"file_size": 1325121498,
"href": "/sequence-files/IGVFFI2373YPAG/@@download/IGVFFI2373YPAG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/72d2e5be-a34a-41a0-bb79-d19bf41f06bc/IGVFFI2373YPAG.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-86_L1_SS-PKR-8_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4646TXRE/",
"accession": "IGVFFI4646TXRE",
"aliases": [
"bradley-bernstein:SS-LS_2418_R2",
"buenrostro-bernstein:SS-LS_2418_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:53:05.693552+00:00",
"file_format": "fastq",
"file_size": 1327560185,
"href": "/sequence-files/IGVFFI4646TXRE/@@download/IGVFFI4646TXRE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/ab3db32b-355b-4415-8ba5-254fa7a4ff71/IGVFFI4646TXRE.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-86_L2_SS-PKR-8_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9887GGFU/",
"accession": "IGVFFI9887GGFU",
"aliases": [
"bradley-bernstein:SS-LS_2418_R1",
"buenrostro-bernstein:SS-LS_2418_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:53:04.708658+00:00",
"file_format": "fastq",
"file_size": 627898416,
"href": "/sequence-files/IGVFFI9887GGFU/@@download/IGVFFI9887GGFU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/a1313f84-0984-4059-80ff-01fc5e007ac5/IGVFFI9887GGFU.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-86_L2_SS-PKR-8_SS-V1-1st-THIRD_R1.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/IGVFDS8346OZIZ/",
"accession": "IGVFDS8346OZIZ",
"status": "released"
}
],
"release_timestamp": "2025-01-14T19:32:36.332882+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM1054BSTI/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1054BSTI",
"aliases": [
"bradley-bernstein:BioSam 4563_SS-PKR 8",
"buenrostro-bernstein:BioSam 4563_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 (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": "2024-02-12T21:23:51.968197+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "e50eaf71-0fdb-4d06-aea0-8503fbfc1f73"
}