{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8995RRJQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8995RRJQ",
"aliases": [
"bradley-bernstein:scRNA Lib 1",
"buenrostro-bernstein:scRNA Lib 1"
],
"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 [IGVFSM5807QDIF](/primary-cells/IGVFSM5807QDIF/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/primary-cells/IGVFSM5807QDIF/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8995RRJQ](/measurement-sets/IGVFDS8995RRJQ/) has sequence file(s): [IGVFFI9142EOMK](/sequence-files/IGVFFI9142EOMK/), [IGVFFI8380WJSO](/sequence-files/IGVFFI8380WJSO/), [IGVFFI2843XQYJ](/sequence-files/IGVFFI2843XQYJ/), [IGVFFI3735QNHK](/sequence-files/IGVFFI3735QNHK/), [IGVFFI1022UPWT](/sequence-files/IGVFFI1022UPWT/), [IGVFFI4385PWNH](/sequence-files/IGVFFI4385PWNH/), [IGVFFI0946QMXK](/sequence-files/IGVFFI0946QMXK/), [IGVFFI2469XRQH](/sequence-files/IGVFFI2469XRQH/), [IGVFFI6832MJFZ](/sequence-files/IGVFFI6832MJFZ/), [IGVFFI7160PIGI](/sequence-files/IGVFFI7160PIGI/), [IGVFFI9534XMFW](/sequence-files/IGVFFI9534XMFW/), [IGVFFI2534TFOM](/sequence-files/IGVFFI2534TFOM/), [IGVFFI2162FUUH](/sequence-files/IGVFFI2162FUUH/), [IGVFFI1910EKSV](/sequence-files/IGVFFI1910EKSV/), [IGVFFI9334UHDO](/sequence-files/IGVFFI9334UHDO/), [IGVFFI7220NOJR](/sequence-files/IGVFFI7220NOJR/) 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/IGVFDS8995RRJQ/"
}
],
"WARNING": [
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS8995RRJQ](/measurement-sets/IGVFDS8995RRJQ/) 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/IGVFDS8995RRJQ/"
}
]
},
"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": "2024-02-12T21:12:20.090027+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/IGVFFI9142EOMK/",
"accession": "IGVFFI9142EOMK",
"aliases": [
"bradley-bernstein:SS-LS_2526_R2",
"buenrostro-bernstein:SS-LS_2526_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:24:33.533476+00:00",
"file_format": "fastq",
"file_size": 1649825064,
"href": "/sequence-files/IGVFFI9142EOMK/@@download/IGVFFI9142EOMK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/695af7e0-f53e-455a-8d41-ca989452769e/IGVFFI9142EOMK.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-2_L4_SS-PKR-1_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8380WJSO/",
"accession": "IGVFFI8380WJSO",
"aliases": [
"bradley-bernstein:SS-LS_1376_R1",
"buenrostro-bernstein:SS-LS_1376_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:23:19.314682+00:00",
"file_format": "fastq",
"file_size": 826502003,
"href": "/sequence-files/IGVFFI8380WJSO/@@download/IGVFFI8380WJSO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/818062ec-d335-4e73-9726-9537bdb75e09/IGVFFI8380WJSO.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-1065_L1_SS-PKR-1_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2843XQYJ/",
"accession": "IGVFFI2843XQYJ",
"aliases": [
"bradley-bernstein:SS-LS_1472_R2",
"buenrostro-bernstein:SS-LS_1472_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:23:57.147959+00:00",
"file_format": "fastq",
"file_size": 2278833445,
"href": "/sequence-files/IGVFFI2843XQYJ/@@download/IGVFFI2843XQYJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/b6b25cc7-c415-4a03-93d2-593f0acfbb0f/IGVFFI2843XQYJ.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-1065_L2_SS-PKR-1_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3735QNHK/",
"accession": "IGVFFI3735QNHK",
"aliases": [
"bradley-bernstein:SS-LS_1376_R2",
"buenrostro-bernstein:SS-LS_1376_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:23:20.233184+00:00",
"file_format": "fastq",
"file_size": 2247370459,
"href": "/sequence-files/IGVFFI3735QNHK/@@download/IGVFFI3735QNHK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/a2e00f31-af95-449a-aa8e-c7860afc272f/IGVFFI3735QNHK.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-1065_L1_SS-PKR-1_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1022UPWT/",
"accession": "IGVFFI1022UPWT",
"aliases": [
"bradley-bernstein:SS-LS_2526_R1",
"buenrostro-bernstein:SS-LS_2526_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:24:32.676602+00:00",
"file_format": "fastq",
"file_size": 679029240,
"href": "/sequence-files/IGVFFI1022UPWT/@@download/IGVFFI1022UPWT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/0f86b3ba-d61b-462b-8155-184a4492af9e/IGVFFI1022UPWT.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-2_L4_SS-PKR-1_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4385PWNH/",
"accession": "IGVFFI4385PWNH",
"aliases": [
"bradley-bernstein:SS-LS_1472_R1",
"buenrostro-bernstein:SS-LS_1472_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:23:55.785751+00:00",
"file_format": "fastq",
"file_size": 839681820,
"href": "/sequence-files/IGVFFI4385PWNH/@@download/IGVFFI4385PWNH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/1ac12a64-d5c9-4a70-94e4-ff929868253f/IGVFFI4385PWNH.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-1065_L2_SS-PKR-1_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0946QMXK/",
"accession": "IGVFFI0946QMXK",
"aliases": [
"bradley-bernstein:SS-LS_1568_R1",
"buenrostro-bernstein:SS-LS_1568_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:32:13.273808+00:00",
"file_format": "fastq",
"file_size": 812436678,
"href": "/sequence-files/IGVFFI0946QMXK/@@download/IGVFFI0946QMXK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/6508c8d2-29ce-4aff-ba20-c8951ad4d861/IGVFFI0946QMXK.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-1065_L3_SS-PKR-1_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2469XRQH/",
"accession": "IGVFFI2469XRQH",
"aliases": [
"bradley-bernstein:SS-LS_1568_R2",
"buenrostro-bernstein:SS-LS_1568_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:32:14.296852+00:00",
"file_format": "fastq",
"file_size": 2217975300,
"href": "/sequence-files/IGVFFI2469XRQH/@@download/IGVFFI2469XRQH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/852e3b01-eefd-4c77-94c0-f8a72fd0f31c/IGVFFI2469XRQH.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-1065_L3_SS-PKR-1_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6832MJFZ/",
"accession": "IGVFFI6832MJFZ",
"aliases": [
"bradley-bernstein:SS-LS_1664_R1",
"buenrostro-bernstein:SS-LS_1664_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:36:42.538539+00:00",
"file_format": "fastq",
"file_size": 805114951,
"href": "/sequence-files/IGVFFI6832MJFZ/@@download/IGVFFI6832MJFZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/ff64199c-c411-442d-95e9-c7047f4268a3/IGVFFI6832MJFZ.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-1065_L4_SS-PKR-1_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7160PIGI/",
"accession": "IGVFFI7160PIGI",
"aliases": [
"bradley-bernstein:SS-LS_1664_R2",
"buenrostro-bernstein:SS-LS_1664_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:36:43.515466+00:00",
"file_format": "fastq",
"file_size": 2220928141,
"href": "/sequence-files/IGVFFI7160PIGI/@@download/IGVFFI7160PIGI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/0c4f60e9-d8b3-4fae-948d-562adc1a37e0/IGVFFI7160PIGI.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-1065_L4_SS-PKR-1_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9534XMFW/",
"accession": "IGVFFI9534XMFW",
"aliases": [
"bradley-bernstein:SS-LS_2238_R1",
"buenrostro-bernstein:SS-LS_2238_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:45:08.707890+00:00",
"file_format": "fastq",
"file_size": 690183089,
"href": "/sequence-files/IGVFFI9534XMFW/@@download/IGVFFI9534XMFW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/5eca6a70-387e-4d99-a56a-7ca373a68aa0/IGVFFI9534XMFW.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-2_L1_SS-PKR-1_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2534TFOM/",
"accession": "IGVFFI2534TFOM",
"aliases": [
"bradley-bernstein:SS-LS_2238_R2",
"buenrostro-bernstein:SS-LS_2238_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:45:09.734873+00:00",
"file_format": "fastq",
"file_size": 1693710051,
"href": "/sequence-files/IGVFFI2534TFOM/@@download/IGVFFI2534TFOM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/859c68af-9fce-47f2-aedd-12dd4312efee/IGVFFI2534TFOM.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-2_L1_SS-PKR-1_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2162FUUH/",
"accession": "IGVFFI2162FUUH",
"aliases": [
"bradley-bernstein:SS-LS_2334_R2",
"buenrostro-bernstein:SS-LS_2334_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:52:34.614792+00:00",
"file_format": "fastq",
"file_size": 1692907520,
"href": "/sequence-files/IGVFFI2162FUUH/@@download/IGVFFI2162FUUH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/75881b48-3047-4e0e-a581-0911c8556161/IGVFFI2162FUUH.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-2_L2_SS-PKR-1_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1910EKSV/",
"accession": "IGVFFI1910EKSV",
"aliases": [
"bradley-bernstein:SS-LS_2430_R1",
"buenrostro-bernstein:SS-LS_2430_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:53:08.584128+00:00",
"file_format": "fastq",
"file_size": 693609056,
"href": "/sequence-files/IGVFFI1910EKSV/@@download/IGVFFI1910EKSV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/c8a78a69-1af9-40fb-a669-9d8598995935/IGVFFI1910EKSV.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-2_L3_SS-PKR-1_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9334UHDO/",
"accession": "IGVFFI9334UHDO",
"aliases": [
"bradley-bernstein:SS-LS_2334_R1",
"buenrostro-bernstein:SS-LS_2334_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:52:33.716981+00:00",
"file_format": "fastq",
"file_size": 698385699,
"href": "/sequence-files/IGVFFI9334UHDO/@@download/IGVFFI9334UHDO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/e4e9fb93-4d8d-4f43-b3ed-b2ba58aa6d6e/IGVFFI9334UHDO.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-2_L2_SS-PKR-1_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7220NOJR/",
"accession": "IGVFFI7220NOJR",
"aliases": [
"bradley-bernstein:SS-LS_2430_R2",
"buenrostro-bernstein:SS-LS_2430_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:53:09.634137+00:00",
"file_format": "fastq",
"file_size": 1681208111,
"href": "/sequence-files/IGVFFI7220NOJR/@@download/IGVFFI7220NOJR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/fd76c166-47e7-41ed-b335-ac21dd86b2ea/IGVFFI7220NOJR.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-2_L3_SS-PKR-1_SS-V1-1st-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/IGVFDS6307SCID/",
"accession": "IGVFDS6307SCID",
"status": "released"
}
],
"release_timestamp": "2025-01-14T19:16:43.919818+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM5807QDIF/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5807QDIF",
"aliases": [
"bradley-bernstein:BioSam 4563_SS-PKR 1",
"buenrostro-bernstein:BioSam 4563_SS-PKR 1"
],
"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 1), 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": "2024-02-12T21:23:19.314682+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "e28ee42c-1eed-42b5-8a89-b10ce54543d8"
}