{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8519RZHK/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8519RZHK",
"aliases": [
"bradley-bernstein:scRNA Lib 29",
"buenrostro-bernstein:scRNA Lib 29"
],
"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 [IGVFDS8519RZHK](/measurement-sets/IGVFDS8519RZHK/) has sequence file(s): [IGVFFI1834ERBD](/sequence-files/IGVFFI1834ERBD/), [IGVFFI4847JKBZ](/sequence-files/IGVFFI4847JKBZ/), [IGVFFI2505WPLF](/sequence-files/IGVFFI2505WPLF/), [IGVFFI6245BUEP](/sequence-files/IGVFFI6245BUEP/), [IGVFFI7941IRQZ](/sequence-files/IGVFFI7941IRQZ/), [IGVFFI5660IUVK](/sequence-files/IGVFFI5660IUVK/), [IGVFFI7946XDFJ](/sequence-files/IGVFFI7946XDFJ/), [IGVFFI0285SCNR](/sequence-files/IGVFFI0285SCNR/), [IGVFFI3962UDVA](/sequence-files/IGVFFI3962UDVA/), [IGVFFI2563VXZM](/sequence-files/IGVFFI2563VXZM/), [IGVFFI9478VJCI](/sequence-files/IGVFFI9478VJCI/), [IGVFFI9436MYSS](/sequence-files/IGVFFI9436MYSS/), [IGVFFI8070MHKG](/sequence-files/IGVFFI8070MHKG/), [IGVFFI4861CZQH](/sequence-files/IGVFFI4861CZQH/), [IGVFFI2533KIUA](/sequence-files/IGVFFI2533KIUA/), [IGVFFI7217SCHT](/sequence-files/IGVFFI7217SCHT/) 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/IGVFDS8519RZHK/"
},
{
"category": "mismatched status",
"detail": "Released primary cell [IGVFSM2899FEKF](/primary-cells/IGVFSM2899FEKF/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/primary-cells/IGVFSM2899FEKF/"
}
],
"WARNING": [
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS8519RZHK](/measurement-sets/IGVFDS8519RZHK/) 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/IGVFDS8519RZHK/"
}
]
},
"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": "2024-02-12T21:13:07.323849+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO2174SHTA/",
"accession": "IGVFDO2174SHTA",
"aliases": [
"bradley-bernstein:Donor 1510",
"buenrostro-bernstein:Donor 1510"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI1834ERBD/",
"accession": "IGVFFI1834ERBD",
"aliases": [
"bradley-bernstein:SS-LS_1528_R1",
"buenrostro-bernstein:SS-LS_1528_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:42:27.041024+00:00",
"file_format": "fastq",
"file_size": 567437697,
"href": "/sequence-files/IGVFFI1834ERBD/@@download/IGVFFI1834ERBD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/61a08f7f-d0f8-4122-bf8b-36a72c9febb7/IGVFFI1834ERBD.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-1121_L2_SS-PKR-5_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4847JKBZ/",
"accession": "IGVFFI4847JKBZ",
"aliases": [
"bradley-bernstein:SS-LS_1432_R2",
"buenrostro-bernstein:SS-LS_1432_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:41:47.744545+00:00",
"file_format": "fastq",
"file_size": 1468817209,
"href": "/sequence-files/IGVFFI4847JKBZ/@@download/IGVFFI4847JKBZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/22cb9396-a980-41d9-bad9-4dcb419f210b/IGVFFI4847JKBZ.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-1121_L1_SS-PKR-5_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2505WPLF/",
"accession": "IGVFFI2505WPLF",
"aliases": [
"bradley-bernstein:SS-LS_1432_R1",
"buenrostro-bernstein:SS-LS_1432_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:41:46.845800+00:00",
"file_format": "fastq",
"file_size": 556349848,
"href": "/sequence-files/IGVFFI2505WPLF/@@download/IGVFFI2505WPLF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/d0ff2cd9-d435-4e10-867e-2bdeee56cfaa/IGVFFI2505WPLF.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-1121_L1_SS-PKR-5_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6245BUEP/",
"accession": "IGVFFI6245BUEP",
"aliases": [
"bradley-bernstein:SS-LS_1528_R2",
"buenrostro-bernstein:SS-LS_1528_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:42:28.109127+00:00",
"file_format": "fastq",
"file_size": 1495748570,
"href": "/sequence-files/IGVFFI6245BUEP/@@download/IGVFFI6245BUEP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/b344327b-0e32-4663-8754-67694edeb000/IGVFFI6245BUEP.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-1121_L2_SS-PKR-5_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7941IRQZ/",
"accession": "IGVFFI7941IRQZ",
"aliases": [
"bradley-bernstein:SS-LS_2294_R2",
"buenrostro-bernstein:SS-LS_2294_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:44:21.972673+00:00",
"file_format": "fastq",
"file_size": 688331343,
"href": "/sequence-files/IGVFFI7941IRQZ/@@download/IGVFFI7941IRQZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/e96057db-e02e-4f08-b7a9-cd1dd78a6f20/IGVFFI7941IRQZ.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-58_L1_SS-PKR-5_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5660IUVK/",
"accession": "IGVFFI5660IUVK",
"aliases": [
"bradley-bernstein:SS-LS_1624_R1",
"buenrostro-bernstein:SS-LS_1624_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:43:05.380418+00:00",
"file_format": "fastq",
"file_size": 550257056,
"href": "/sequence-files/IGVFFI5660IUVK/@@download/IGVFFI5660IUVK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/2469bba5-6996-4cc1-8347-15ff40523eed/IGVFFI5660IUVK.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-1121_L3_SS-PKR-5_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7946XDFJ/",
"accession": "IGVFFI7946XDFJ",
"aliases": [
"bradley-bernstein:SS-LS_2294_R1",
"buenrostro-bernstein:SS-LS_2294_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:44:20.392549+00:00",
"file_format": "fastq",
"file_size": 290250348,
"href": "/sequence-files/IGVFFI7946XDFJ/@@download/IGVFFI7946XDFJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/3ed0005b-67de-4d88-b05a-57bbae2d07e8/IGVFFI7946XDFJ.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-58_L1_SS-PKR-5_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0285SCNR/",
"accession": "IGVFFI0285SCNR",
"aliases": [
"bradley-bernstein:SS-LS_2390_R1",
"buenrostro-bernstein:SS-LS_2390_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:45:24.028903+00:00",
"file_format": "fastq",
"file_size": 292302690,
"href": "/sequence-files/IGVFFI0285SCNR/@@download/IGVFFI0285SCNR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/9e466124-1d75-4446-8f40-8ac539007c38/IGVFFI0285SCNR.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-58_L2_SS-PKR-5_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3962UDVA/",
"accession": "IGVFFI3962UDVA",
"aliases": [
"bradley-bernstein:SS-LS_1624_R2",
"buenrostro-bernstein:SS-LS_1624_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:43:06.509617+00:00",
"file_format": "fastq",
"file_size": 1457441997,
"href": "/sequence-files/IGVFFI3962UDVA/@@download/IGVFFI3962UDVA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/84f0b74d-43a6-414b-af91-205055c052cb/IGVFFI3962UDVA.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-1121_L3_SS-PKR-5_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2563VXZM/",
"accession": "IGVFFI2563VXZM",
"aliases": [
"bradley-bernstein:SS-LS_2486_R2",
"buenrostro-bernstein:SS-LS_2486_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:46:04.265056+00:00",
"file_format": "fastq",
"file_size": 681890471,
"href": "/sequence-files/IGVFFI2563VXZM/@@download/IGVFFI2563VXZM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/49b6e52e-8d70-429e-8b01-00dc6841f2a9/IGVFFI2563VXZM.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-58_L3_SS-PKR-5_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9478VJCI/",
"accession": "IGVFFI9478VJCI",
"aliases": [
"bradley-bernstein:SS-LS_2390_R2",
"buenrostro-bernstein:SS-LS_2390_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:45:24.936921+00:00",
"file_format": "fastq",
"file_size": 685178231,
"href": "/sequence-files/IGVFFI9478VJCI/@@download/IGVFFI9478VJCI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/e7aea004-c5c5-4ac2-9bfc-02d19f88d6a0/IGVFFI9478VJCI.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-58_L2_SS-PKR-5_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9436MYSS/",
"accession": "IGVFFI9436MYSS",
"aliases": [
"bradley-bernstein:SS-LS_1720_R1",
"buenrostro-bernstein:SS-LS_1720_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:43:40.595046+00:00",
"file_format": "fastq",
"file_size": 551632329,
"href": "/sequence-files/IGVFFI9436MYSS/@@download/IGVFFI9436MYSS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/fbbb0f76-442a-44ba-9093-906ae47a15a1/IGVFFI9436MYSS.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-1121_L4_SS-PKR-5_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8070MHKG/",
"accession": "IGVFFI8070MHKG",
"aliases": [
"bradley-bernstein:SS-LS_1720_R2",
"buenrostro-bernstein:SS-LS_1720_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:43:41.765103+00:00",
"file_format": "fastq",
"file_size": 1481119785,
"href": "/sequence-files/IGVFFI8070MHKG/@@download/IGVFFI8070MHKG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/8aa9b918-c653-445b-a08c-e269025b6ceb/IGVFFI8070MHKG.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-1121_L4_SS-PKR-5_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4861CZQH/",
"accession": "IGVFFI4861CZQH",
"aliases": [
"bradley-bernstein:SS-LS_2486_R1",
"buenrostro-bernstein:SS-LS_2486_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:46:03.142713+00:00",
"file_format": "fastq",
"file_size": 290913013,
"href": "/sequence-files/IGVFFI4861CZQH/@@download/IGVFFI4861CZQH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/b83956dd-e9b2-4f07-99d2-c41dddf51fee/IGVFFI4861CZQH.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-58_L3_SS-PKR-5_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2533KIUA/",
"accession": "IGVFFI2533KIUA",
"aliases": [
"bradley-bernstein:SS-LS_2582_R1",
"buenrostro-bernstein:SS-LS_2582_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:46:40.845949+00:00",
"file_format": "fastq",
"file_size": 286702075,
"href": "/sequence-files/IGVFFI2533KIUA/@@download/IGVFFI2533KIUA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/8b7a4b7e-aba4-48b7-b1fa-4e55739faedc/IGVFFI2533KIUA.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-58_L4_SS-PKR-5_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7217SCHT/",
"accession": "IGVFFI7217SCHT",
"aliases": [
"bradley-bernstein:SS-LS_2582_R2",
"buenrostro-bernstein:SS-LS_2582_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:46:43.028950+00:00",
"file_format": "fastq",
"file_size": 673380484,
"href": "/sequence-files/IGVFFI7217SCHT/@@download/IGVFFI7217SCHT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/ac147e50-349a-4a66-8939-751bc9e749ec/IGVFFI7217SCHT.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-58_L4_SS-PKR-5_SS-V2-PLATE2-2nd-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/IGVFDS5496ZDEU/",
"accession": "IGVFDS5496ZDEU",
"status": "released"
}
],
"release_timestamp": "2025-01-14T19:39:40.926775+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM2899FEKF/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2899FEKF",
"aliases": [
"bradley-bernstein:BioSam 4567_SS-PKR 5",
"buenrostro-bernstein:BioSam 4567_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 (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": "2024-02-12T21:41:46.845800+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "39a5ed13-49eb-44a3-ba51-ec20b3b21be6"
}