{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6493BIXB/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6493BIXB",
"aliases": [
"bradley-bernstein:scRNA Lib 44",
"buenrostro-bernstein:scRNA Lib 44"
],
"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 [IGVFDS6493BIXB](/measurement-sets/IGVFDS6493BIXB/) has sequence file(s): [IGVFFI9021ZOJQ](/sequence-files/IGVFFI9021ZOJQ/), [IGVFFI2260OFTA](/sequence-files/IGVFFI2260OFTA/), [IGVFFI9668HPPB](/sequence-files/IGVFFI9668HPPB/), [IGVFFI7683RRAY](/sequence-files/IGVFFI7683RRAY/), [IGVFFI9516VAJN](/sequence-files/IGVFFI9516VAJN/), [IGVFFI9094AVDM](/sequence-files/IGVFFI9094AVDM/), [IGVFFI1561VUEK](/sequence-files/IGVFFI1561VUEK/), [IGVFFI8376EUAE](/sequence-files/IGVFFI8376EUAE/), [IGVFFI0197TCOD](/sequence-files/IGVFFI0197TCOD/), [IGVFFI3131UBYL](/sequence-files/IGVFFI3131UBYL/), [IGVFFI8088DYSQ](/sequence-files/IGVFFI8088DYSQ/), [IGVFFI9202VUAM](/sequence-files/IGVFFI9202VUAM/), [IGVFFI2721SLXK](/sequence-files/IGVFFI2721SLXK/), [IGVFFI0820HHDP](/sequence-files/IGVFFI0820HHDP/), [IGVFFI7710NGVV](/sequence-files/IGVFFI7710NGVV/), [IGVFFI8294EFUQ](/sequence-files/IGVFFI8294EFUQ/) 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/IGVFDS6493BIXB/"
},
{
"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 [IGVFDS6493BIXB](/measurement-sets/IGVFDS6493BIXB/) 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/IGVFDS6493BIXB/"
}
]
},
"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": "2024-02-12T21:12:39.339722+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/IGVFFI9021ZOJQ/",
"accession": "IGVFFI9021ZOJQ",
"aliases": [
"bradley-bernstein:SS-LS_1462_R2",
"buenrostro-bernstein:SS-LS_1462_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:25:45.476013+00:00",
"file_format": "fastq",
"file_size": 2602489982,
"href": "/sequence-files/IGVFFI9021ZOJQ/@@download/IGVFFI9021ZOJQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/a92a73ab-b740-4cbc-bba9-633b5ffdc27c/IGVFFI9021ZOJQ.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-1151_L1_SS-PKR-8_SS-V1-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2260OFTA/",
"accession": "IGVFFI2260OFTA",
"aliases": [
"bradley-bernstein:SS-LS_1558_R2",
"buenrostro-bernstein:SS-LS_1558_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:26:20.442842+00:00",
"file_format": "fastq",
"file_size": 2639784077,
"href": "/sequence-files/IGVFFI2260OFTA/@@download/IGVFFI2260OFTA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/7715f4cf-a828-4dbb-b972-e363b6f786fc/IGVFFI2260OFTA.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-1151_L2_SS-PKR-8_SS-V1-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9668HPPB/",
"accession": "IGVFFI9668HPPB",
"aliases": [
"bradley-bernstein:SS-LS_1462_R1",
"buenrostro-bernstein:SS-LS_1462_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:25:44.159009+00:00",
"file_format": "fastq",
"file_size": 1101623249,
"href": "/sequence-files/IGVFFI9668HPPB/@@download/IGVFFI9668HPPB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/b1418324-ea6c-4ac6-b528-7a093b19acc4/IGVFFI9668HPPB.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-1151_L1_SS-PKR-8_SS-V1-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7683RRAY/",
"accession": "IGVFFI7683RRAY",
"aliases": [
"bradley-bernstein:SS-LS_2420_R1",
"buenrostro-bernstein:SS-LS_2420_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:29:09.840577+00:00",
"file_format": "fastq",
"file_size": 577630012,
"href": "/sequence-files/IGVFFI7683RRAY/@@download/IGVFFI7683RRAY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/2764d6f2-01cb-4c61-b18f-40a8fe65e879/IGVFFI7683RRAY.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-88_L2_SS-PKR-8_SS-V1-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9516VAJN/",
"accession": "IGVFFI9516VAJN",
"aliases": [
"bradley-bernstein:SS-LS_2516_R1",
"buenrostro-bernstein:SS-LS_2516_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:29:44.191750+00:00",
"file_format": "fastq",
"file_size": 575028151,
"href": "/sequence-files/IGVFFI9516VAJN/@@download/IGVFFI9516VAJN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/26df44c0-c894-46ba-8618-860879ced8b8/IGVFFI9516VAJN.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-88_L3_SS-PKR-8_SS-V1-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9094AVDM/",
"accession": "IGVFFI9094AVDM",
"aliases": [
"bradley-bernstein:SS-LS_1654_R2",
"buenrostro-bernstein:SS-LS_1654_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:26:57.508388+00:00",
"file_format": "fastq",
"file_size": 2591461720,
"href": "/sequence-files/IGVFFI9094AVDM/@@download/IGVFFI9094AVDM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/0556a359-fdcf-4d7f-b517-c7b3845f0789/IGVFFI9094AVDM.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-1151_L3_SS-PKR-8_SS-V1-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1561VUEK/",
"accession": "IGVFFI1561VUEK",
"aliases": [
"bradley-bernstein:SS-LS_2420_R2",
"buenrostro-bernstein:SS-LS_2420_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:29:10.813855+00:00",
"file_format": "fastq",
"file_size": 1220220637,
"href": "/sequence-files/IGVFFI1561VUEK/@@download/IGVFFI1561VUEK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/60bb3c9f-2344-4c32-a123-c6e31affb72c/IGVFFI1561VUEK.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-88_L2_SS-PKR-8_SS-V1-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8376EUAE/",
"accession": "IGVFFI8376EUAE",
"aliases": [
"bradley-bernstein:SS-LS_1558_R1",
"buenrostro-bernstein:SS-LS_1558_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:26:19.473652+00:00",
"file_format": "fastq",
"file_size": 1115709372,
"href": "/sequence-files/IGVFFI8376EUAE/@@download/IGVFFI8376EUAE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/58f68b5e-4d6f-45ba-b435-25f2587ef6e4/IGVFFI8376EUAE.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-1151_L2_SS-PKR-8_SS-V1-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0197TCOD/",
"accession": "IGVFFI0197TCOD",
"aliases": [
"bradley-bernstein:SS-LS_1750_R1",
"buenrostro-bernstein:SS-LS_1750_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:27:33.571379+00:00",
"file_format": "fastq",
"file_size": 1116119703,
"href": "/sequence-files/IGVFFI0197TCOD/@@download/IGVFFI0197TCOD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/e48fd52d-e438-4c59-8da2-016f6f096960/IGVFFI0197TCOD.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-1151_L4_SS-PKR-8_SS-V1-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3131UBYL/",
"accession": "IGVFFI3131UBYL",
"aliases": [
"bradley-bernstein:SS-LS_1750_R2",
"buenrostro-bernstein:SS-LS_1750_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:27:34.577965+00:00",
"file_format": "fastq",
"file_size": 2638896618,
"href": "/sequence-files/IGVFFI3131UBYL/@@download/IGVFFI3131UBYL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/78dc757f-d7be-4bbb-a872-3ae6b610d4c2/IGVFFI3131UBYL.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-1151_L4_SS-PKR-8_SS-V1-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8088DYSQ/",
"accession": "IGVFFI8088DYSQ",
"aliases": [
"bradley-bernstein:SS-LS_2612_R1",
"buenrostro-bernstein:SS-LS_2612_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:30:22.261805+00:00",
"file_format": "fastq",
"file_size": 565361883,
"href": "/sequence-files/IGVFFI8088DYSQ/@@download/IGVFFI8088DYSQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/37cc9408-ef02-4fa8-8888-4efa59edc2ac/IGVFFI8088DYSQ.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-88_L4_SS-PKR-8_SS-V1-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9202VUAM/",
"accession": "IGVFFI9202VUAM",
"aliases": [
"bradley-bernstein:SS-LS_2612_R2",
"buenrostro-bernstein:SS-LS_2612_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:30:23.190662+00:00",
"file_format": "fastq",
"file_size": 1198397611,
"href": "/sequence-files/IGVFFI9202VUAM/@@download/IGVFFI9202VUAM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/8e8536b1-0b0f-4421-9f20-08e98afb05c2/IGVFFI9202VUAM.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-88_L4_SS-PKR-8_SS-V1-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2721SLXK/",
"accession": "IGVFFI2721SLXK",
"aliases": [
"bradley-bernstein:SS-LS_1654_R1",
"buenrostro-bernstein:SS-LS_1654_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:26:56.553924+00:00",
"file_format": "fastq",
"file_size": 1099623537,
"href": "/sequence-files/IGVFFI2721SLXK/@@download/IGVFFI2721SLXK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/5f9cf8ec-c719-4452-9d53-dcc0fabbbd48/IGVFFI2721SLXK.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-1151_L3_SS-PKR-8_SS-V1-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0820HHDP/",
"accession": "IGVFFI0820HHDP",
"aliases": [
"bradley-bernstein:SS-LS_2324_R2",
"buenrostro-bernstein:SS-LS_2324_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:28:31.692703+00:00",
"file_format": "fastq",
"file_size": 1217681861,
"href": "/sequence-files/IGVFFI0820HHDP/@@download/IGVFFI0820HHDP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/d7bfc5ae-d55d-47e2-b1e2-3db2171528bd/IGVFFI0820HHDP.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-88_L1_SS-PKR-8_SS-V1-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7710NGVV/",
"accession": "IGVFFI7710NGVV",
"aliases": [
"bradley-bernstein:SS-LS_2324_R1",
"buenrostro-bernstein:SS-LS_2324_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:28:30.713910+00:00",
"file_format": "fastq",
"file_size": 576608560,
"href": "/sequence-files/IGVFFI7710NGVV/@@download/IGVFFI7710NGVV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/06b77f33-1061-4815-b45f-81405a7f36bd/IGVFFI7710NGVV.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-88_L1_SS-PKR-8_SS-V1-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8294EFUQ/",
"accession": "IGVFFI8294EFUQ",
"aliases": [
"bradley-bernstein:SS-LS_2516_R2",
"buenrostro-bernstein:SS-LS_2516_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:29:45.235132+00:00",
"file_format": "fastq",
"file_size": 1213248999,
"href": "/sequence-files/IGVFFI8294EFUQ/@@download/IGVFFI8294EFUQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/598c1079-c150-4fc2-836e-59c12cc52043/IGVFFI8294EFUQ.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-88_L3_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/IGVFDS0726CKKN/",
"accession": "IGVFDS0726CKKN",
"status": "released"
}
],
"release_timestamp": "2025-01-14T18:22:59.298939+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": "2024-02-12T21:25:44.159009+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "fa2e335a-ad65-4675-a0f6-12fc47588614"
}