{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2451WVVC/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2451WVVC",
"aliases": [
"bradley-bernstein:scATAC Lib 11",
"buenrostro-bernstein:scATAC Lib 11"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002764/",
"status": "released",
"term_name": "single-cell ATAC-seq"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released primary cell [IGVFSM6909NWSZ](/primary-cells/IGVFSM6909NWSZ/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/primary-cells/IGVFSM6909NWSZ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2451WVVC](/measurement-sets/IGVFDS2451WVVC/) has sequence file(s): [IGVFFI6140GLMX](/sequence-files/IGVFFI6140GLMX/), [IGVFFI3138MPIQ](/sequence-files/IGVFFI3138MPIQ/), [IGVFFI9632MVNQ](/sequence-files/IGVFFI9632MVNQ/), [IGVFFI3815ENHO](/sequence-files/IGVFFI3815ENHO/), [IGVFFI6007KVXA](/sequence-files/IGVFFI6007KVXA/), [IGVFFI4771FRPL](/sequence-files/IGVFFI4771FRPL/), [IGVFFI3237TNAU](/sequence-files/IGVFFI3237TNAU/), [IGVFFI1667CBYV](/sequence-files/IGVFFI1667CBYV/), [IGVFFI9988RMIX](/sequence-files/IGVFFI9988RMIX/), [IGVFFI0753TASH](/sequence-files/IGVFFI0753TASH/), [IGVFFI2717TEHD](/sequence-files/IGVFFI2717TEHD/), [IGVFFI6227MHJN](/sequence-files/IGVFFI6227MHJN/), [IGVFFI7055MRMG](/sequence-files/IGVFFI7055MRMG/), [IGVFFI4430SPNE](/sequence-files/IGVFFI4430SPNE/), [IGVFFI7633OCKQ](/sequence-files/IGVFFI7633OCKQ/), [IGVFFI1382FFYF](/sequence-files/IGVFFI1382FFYF/) 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/IGVFDS2451WVVC/"
}
],
"WARNING": [
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS2451WVVC](/measurement-sets/IGVFDS2451WVVC/) has an `assay_term` of single-cell ATAC-seq 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/IGVFDS2451WVVC/"
}
]
},
"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": "2024-02-12T21:13:02.003867+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/IGVFFI6140GLMX/",
"accession": "IGVFFI6140GLMX",
"aliases": [
"bradley-bernstein:SS-LS_1491_R2",
"buenrostro-bernstein:SS-LS_1491_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:42:12.237597+00:00",
"file_format": "fastq",
"file_size": 8875,
"href": "/sequence-files/IGVFFI6140GLMX/@@download/IGVFFI6140GLMX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/82fefee4-356b-4531-8c39-5a61bc8a9852/IGVFFI6140GLMX.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-1084_L2_SS-PKR-2_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3138MPIQ/",
"accession": "IGVFFI3138MPIQ",
"aliases": [
"bradley-bernstein:SS-LS_1491_R1",
"buenrostro-bernstein:SS-LS_1491_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:42:11.228535+00:00",
"file_format": "fastq",
"file_size": 5220,
"href": "/sequence-files/IGVFFI3138MPIQ/@@download/IGVFFI3138MPIQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/8bfe3327-74a2-4ac5-8f57-1be63857b22d/IGVFFI3138MPIQ.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-1084_L2_SS-PKR-2_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9632MVNQ/",
"accession": "IGVFFI9632MVNQ",
"aliases": [
"bradley-bernstein:SS-LS_1587_R2",
"buenrostro-bernstein:SS-LS_1587_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:42:49.179563+00:00",
"file_format": "fastq",
"file_size": 8318,
"href": "/sequence-files/IGVFFI9632MVNQ/@@download/IGVFFI9632MVNQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/e16abd22-372f-4c46-93ec-631e271a0642/IGVFFI9632MVNQ.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-1084_L3_SS-PKR-2_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3815ENHO/",
"accession": "IGVFFI3815ENHO",
"aliases": [
"bradley-bernstein:SS-LS_1395_R2",
"buenrostro-bernstein:SS-LS_1395_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:41:31.783768+00:00",
"file_format": "fastq",
"file_size": 9206,
"href": "/sequence-files/IGVFFI3815ENHO/@@download/IGVFFI3815ENHO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/205dd148-3a2c-4104-b9ab-b28bde2ef2af/IGVFFI3815ENHO.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-1084_L1_SS-PKR-2_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6007KVXA/",
"accession": "IGVFFI6007KVXA",
"aliases": [
"bradley-bernstein:SS-LS_2257_R2",
"buenrostro-bernstein:SS-LS_2257_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:44:04.065534+00:00",
"file_format": "fastq",
"file_size": 363212022,
"href": "/sequence-files/IGVFFI6007KVXA/@@download/IGVFFI6007KVXA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/2f448c8b-2881-40c0-b3fe-805852583881/IGVFFI6007KVXA.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-21_L1_SS-PKR-2_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4771FRPL/",
"accession": "IGVFFI4771FRPL",
"aliases": [
"bradley-bernstein:SS-LS_1395_R1",
"buenrostro-bernstein:SS-LS_1395_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:41:30.869294+00:00",
"file_format": "fastq",
"file_size": 5344,
"href": "/sequence-files/IGVFFI4771FRPL/@@download/IGVFFI4771FRPL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/ee73e425-dfe3-46ba-a49f-3e3dfce3623e/IGVFFI4771FRPL.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-1084_L1_SS-PKR-2_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3237TNAU/",
"accession": "IGVFFI3237TNAU",
"aliases": [
"bradley-bernstein:SS-LS_1587_R1",
"buenrostro-bernstein:SS-LS_1587_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:42:48.280399+00:00",
"file_format": "fastq",
"file_size": 4908,
"href": "/sequence-files/IGVFFI3237TNAU/@@download/IGVFFI3237TNAU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/a4bc718c-536c-44e4-8f3c-f849b75616bb/IGVFFI3237TNAU.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-1084_L3_SS-PKR-2_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1667CBYV/",
"accession": "IGVFFI1667CBYV",
"aliases": [
"bradley-bernstein:SS-LS_2353_R1",
"buenrostro-bernstein:SS-LS_2353_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:44:41.169590+00:00",
"file_format": "fastq",
"file_size": 213747590,
"href": "/sequence-files/IGVFFI1667CBYV/@@download/IGVFFI1667CBYV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/cd4baa55-bcce-4f8e-9654-6b05febc08d7/IGVFFI1667CBYV.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-21_L2_SS-PKR-2_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9988RMIX/",
"accession": "IGVFFI9988RMIX",
"aliases": [
"bradley-bernstein:SS-LS_2353_R2",
"buenrostro-bernstein:SS-LS_2353_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:44:42.156726+00:00",
"file_format": "fastq",
"file_size": 364826132,
"href": "/sequence-files/IGVFFI9988RMIX/@@download/IGVFFI9988RMIX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/38b8ae0f-fe5e-40d5-b04c-75a9bb9b38c3/IGVFFI9988RMIX.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-21_L2_SS-PKR-2_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0753TASH/",
"accession": "IGVFFI0753TASH",
"aliases": [
"bradley-bernstein:SS-LS_1683_R1",
"buenrostro-bernstein:SS-LS_1683_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:43:25.731336+00:00",
"file_format": "fastq",
"file_size": 5773,
"href": "/sequence-files/IGVFFI0753TASH/@@download/IGVFFI0753TASH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/f2076d87-a06b-4507-ad91-cfccc759b460/IGVFFI0753TASH.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-1084_L4_SS-PKR-2_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2717TEHD/",
"accession": "IGVFFI2717TEHD",
"aliases": [
"bradley-bernstein:SS-LS_1683_R2",
"buenrostro-bernstein:SS-LS_1683_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:43:26.669569+00:00",
"file_format": "fastq",
"file_size": 9726,
"href": "/sequence-files/IGVFFI2717TEHD/@@download/IGVFFI2717TEHD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/aba6041a-4fec-4800-a5ce-e2772cce23cf/IGVFFI2717TEHD.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-1084_L4_SS-PKR-2_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6227MHJN/",
"accession": "IGVFFI6227MHJN",
"aliases": [
"bradley-bernstein:SS-LS_2257_R1",
"buenrostro-bernstein:SS-LS_2257_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:44:02.825052+00:00",
"file_format": "fastq",
"file_size": 212630179,
"href": "/sequence-files/IGVFFI6227MHJN/@@download/IGVFFI6227MHJN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/83455595-c581-4280-adc8-2ddd8ac67d88/IGVFFI6227MHJN.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-21_L1_SS-PKR-2_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7055MRMG/",
"accession": "IGVFFI7055MRMG",
"aliases": [
"bradley-bernstein:SS-LS_2449_R2",
"buenrostro-bernstein:SS-LS_2449_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:45:47.480794+00:00",
"file_format": "fastq",
"file_size": 362274559,
"href": "/sequence-files/IGVFFI7055MRMG/@@download/IGVFFI7055MRMG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/848990c3-ba2d-452b-bb44-bf46e59c4e7f/IGVFFI7055MRMG.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-21_L3_SS-PKR-2_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4430SPNE/",
"accession": "IGVFFI4430SPNE",
"aliases": [
"bradley-bernstein:SS-LS_2545_R1",
"buenrostro-bernstein:SS-LS_2545_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:46:24.406476+00:00",
"file_format": "fastq",
"file_size": 211554713,
"href": "/sequence-files/IGVFFI4430SPNE/@@download/IGVFFI4430SPNE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/ad5c690d-22ff-40e5-b270-51836f9c1a38/IGVFFI4430SPNE.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-21_L4_SS-PKR-2_SS-V2-PLATE2-2nd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7633OCKQ/",
"accession": "IGVFFI7633OCKQ",
"aliases": [
"bradley-bernstein:SS-LS_2545_R2",
"buenrostro-bernstein:SS-LS_2545_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:46:25.459326+00:00",
"file_format": "fastq",
"file_size": 361429484,
"href": "/sequence-files/IGVFFI7633OCKQ/@@download/IGVFFI7633OCKQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/a00014c5-4b8b-4b28-8f10-6338c0ccc044/IGVFFI7633OCKQ.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-21_L4_SS-PKR-2_SS-V2-PLATE2-2nd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1382FFYF/",
"accession": "IGVFFI1382FFYF",
"aliases": [
"bradley-bernstein:SS-LS_2449_R1",
"buenrostro-bernstein:SS-LS_2449_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:45:46.524855+00:00",
"file_format": "fastq",
"file_size": 212639879,
"href": "/sequence-files/IGVFFI1382FFYF/@@download/IGVFFI1382FFYF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/9f9fd231-6155-4f2b-8c49-813e6316a1a6/IGVFFI1382FFYF.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-21_L3_SS-PKR-2_SS-V2-PLATE2-2nd-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/IGVFDS8460SRNI/",
"accession": "IGVFDS8460SRNI",
"status": "released"
}
],
"release_timestamp": "2025-01-14T19:30:32.837413+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM6909NWSZ/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6909NWSZ",
"aliases": [
"bradley-bernstein:BioSam 4567_SS-PKR 2",
"buenrostro-bernstein:BioSam 4567_SS-PKR 2"
],
"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 2), 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": "2024-02-12T21:41:30.869294+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "627988ae-39dc-41e8-889a-24ea683ecd88"
}