{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4920HAWH/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4920HAWH",
"aliases": [
"bradley-bernstein:scATAC Lib 13",
"buenrostro-bernstein:scATAC Lib 13"
],
"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 [IGVFSM6852UYUG](/primary-cells/IGVFSM6852UYUG/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/primary-cells/IGVFSM6852UYUG/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4920HAWH](/measurement-sets/IGVFDS4920HAWH/) has sequence file(s): [IGVFFI2980NFYV](/sequence-files/IGVFFI2980NFYV/), [IGVFFI6228FWZD](/sequence-files/IGVFFI6228FWZD/), [IGVFFI2527JXZX](/sequence-files/IGVFFI2527JXZX/), [IGVFFI4672PTIU](/sequence-files/IGVFFI4672PTIU/), [IGVFFI6508OWEB](/sequence-files/IGVFFI6508OWEB/), [IGVFFI9822FZHJ](/sequence-files/IGVFFI9822FZHJ/), [IGVFFI2614PYXV](/sequence-files/IGVFFI2614PYXV/), [IGVFFI4669ZMEU](/sequence-files/IGVFFI4669ZMEU/), [IGVFFI3561JSUE](/sequence-files/IGVFFI3561JSUE/), [IGVFFI5168CLXA](/sequence-files/IGVFFI5168CLXA/), [IGVFFI6197FOYC](/sequence-files/IGVFFI6197FOYC/), [IGVFFI9375XKVX](/sequence-files/IGVFFI9375XKVX/), [IGVFFI1130YVEO](/sequence-files/IGVFFI1130YVEO/), [IGVFFI2375DWZC](/sequence-files/IGVFFI2375DWZC/), [IGVFFI4988JVYK](/sequence-files/IGVFFI4988JVYK/), [IGVFFI0562AOML](/sequence-files/IGVFFI0562AOML/) 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/IGVFDS4920HAWH/"
}
],
"WARNING": [
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS4920HAWH](/measurement-sets/IGVFDS4920HAWH/) 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/IGVFDS4920HAWH/"
}
]
},
"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": "2024-02-12T21:12:22.348717+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/IGVFFI2980NFYV/",
"accession": "IGVFFI2980NFYV",
"aliases": [
"bradley-bernstein:SS-LS_1399_R2",
"buenrostro-bernstein:SS-LS_1399_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:23:27.063192+00:00",
"file_format": "fastq",
"file_size": 2260,
"href": "/sequence-files/IGVFFI2980NFYV/@@download/IGVFFI2980NFYV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/3f4f65b9-5715-47ba-8500-2b2f3fc8351b/IGVFFI2980NFYV.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-1088_L1_SS-PKR-3_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6228FWZD/",
"accession": "IGVFFI6228FWZD",
"aliases": [
"bradley-bernstein:SS-LS_1399_R1",
"buenrostro-bernstein:SS-LS_1399_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:23:26.123062+00:00",
"file_format": "fastq",
"file_size": 1312,
"href": "/sequence-files/IGVFFI6228FWZD/@@download/IGVFFI6228FWZD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/7590e6d1-79fd-45e8-9ff8-a9934d214f55/IGVFFI6228FWZD.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-1088_L1_SS-PKR-3_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2527JXZX/",
"accession": "IGVFFI2527JXZX",
"aliases": [
"bradley-bernstein:SS-LS_2453_R1",
"buenrostro-bernstein:SS-LS_2453_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:24:04.472423+00:00",
"file_format": "fastq",
"file_size": 549930814,
"href": "/sequence-files/IGVFFI2527JXZX/@@download/IGVFFI2527JXZX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/8044f2a3-4585-4227-8c10-415c39a7d950/IGVFFI2527JXZX.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-25_L3_SS-PKR-3_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4672PTIU/",
"accession": "IGVFFI4672PTIU",
"aliases": [
"bradley-bernstein:SS-LS_2453_R2",
"buenrostro-bernstein:SS-LS_2453_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:24:05.576429+00:00",
"file_format": "fastq",
"file_size": 939472217,
"href": "/sequence-files/IGVFFI4672PTIU/@@download/IGVFFI4672PTIU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/9cbdb126-77da-4f28-a608-9dce4f712433/IGVFFI4672PTIU.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-25_L3_SS-PKR-3_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6508OWEB/",
"accession": "IGVFFI6508OWEB",
"aliases": [
"bradley-bernstein:SS-LS_2549_R1",
"buenrostro-bernstein:SS-LS_2549_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:24:38.953693+00:00",
"file_format": "fastq",
"file_size": 545301610,
"href": "/sequence-files/IGVFFI6508OWEB/@@download/IGVFFI6508OWEB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/f682160d-17af-4d7f-8af1-13b3aff5141f/IGVFFI6508OWEB.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-25_L4_SS-PKR-3_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9822FZHJ/",
"accession": "IGVFFI9822FZHJ",
"aliases": [
"bradley-bernstein:SS-LS_2549_R2",
"buenrostro-bernstein:SS-LS_2549_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:24:39.842863+00:00",
"file_format": "fastq",
"file_size": 933938487,
"href": "/sequence-files/IGVFFI9822FZHJ/@@download/IGVFFI9822FZHJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/8015930b-db83-4171-9de9-fcb0b951f8bd/IGVFFI9822FZHJ.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-25_L4_SS-PKR-3_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2614PYXV/",
"accession": "IGVFFI2614PYXV",
"aliases": [
"bradley-bernstein:SS-LS_1495_R1",
"buenrostro-bernstein:SS-LS_1495_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:27:54.295210+00:00",
"file_format": "fastq",
"file_size": 1229,
"href": "/sequence-files/IGVFFI2614PYXV/@@download/IGVFFI2614PYXV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/2beeae7c-0097-44ce-ad2c-d4331d4e97ab/IGVFFI2614PYXV.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-1088_L2_SS-PKR-3_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4669ZMEU/",
"accession": "IGVFFI4669ZMEU",
"aliases": [
"bradley-bernstein:SS-LS_1495_R2",
"buenrostro-bernstein:SS-LS_1495_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:27:55.339595+00:00",
"file_format": "fastq",
"file_size": 2154,
"href": "/sequence-files/IGVFFI4669ZMEU/@@download/IGVFFI4669ZMEU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/0c8cf230-fb6d-49b1-acdb-973ea293210e/IGVFFI4669ZMEU.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-1088_L2_SS-PKR-3_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3561JSUE/",
"accession": "IGVFFI3561JSUE",
"aliases": [
"bradley-bernstein:SS-LS_1591_R2",
"buenrostro-bernstein:SS-LS_1591_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:32:20.345240+00:00",
"file_format": "fastq",
"file_size": 2979,
"href": "/sequence-files/IGVFFI3561JSUE/@@download/IGVFFI3561JSUE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/3cf051c1-5e44-4a89-a1cf-da802d3686d1/IGVFFI3561JSUE.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-1088_L3_SS-PKR-3_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5168CLXA/",
"accession": "IGVFFI5168CLXA",
"aliases": [
"bradley-bernstein:SS-LS_1591_R1",
"buenrostro-bernstein:SS-LS_1591_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:32:19.430809+00:00",
"file_format": "fastq",
"file_size": 1726,
"href": "/sequence-files/IGVFFI5168CLXA/@@download/IGVFFI5168CLXA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/7fdbd92c-e74c-4651-8966-41a88060594b/IGVFFI5168CLXA.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-1088_L3_SS-PKR-3_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6197FOYC/",
"accession": "IGVFFI6197FOYC",
"aliases": [
"bradley-bernstein:SS-LS_1687_R2",
"buenrostro-bernstein:SS-LS_1687_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:40:40.570948+00:00",
"file_format": "fastq",
"file_size": 2529,
"href": "/sequence-files/IGVFFI6197FOYC/@@download/IGVFFI6197FOYC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/09c35183-3a14-47bf-88b1-02c46280aab3/IGVFFI6197FOYC.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-1088_L4_SS-PKR-3_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9375XKVX/",
"accession": "IGVFFI9375XKVX",
"aliases": [
"bradley-bernstein:SS-LS_1687_R1",
"buenrostro-bernstein:SS-LS_1687_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:40:39.595226+00:00",
"file_format": "fastq",
"file_size": 1469,
"href": "/sequence-files/IGVFFI9375XKVX/@@download/IGVFFI9375XKVX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/3730e6b4-5e2a-4802-94a3-f420c34a2ded/IGVFFI9375XKVX.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-1088_L4_SS-PKR-3_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1130YVEO/",
"accession": "IGVFFI1130YVEO",
"aliases": [
"bradley-bernstein:SS-LS_2261_R1",
"buenrostro-bernstein:SS-LS_2261_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:45:14.504148+00:00",
"file_format": "fastq",
"file_size": 548495549,
"href": "/sequence-files/IGVFFI1130YVEO/@@download/IGVFFI1130YVEO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/3a57020a-b63d-4e35-97cd-eae1b24b9d54/IGVFFI1130YVEO.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-25_L1_SS-PKR-3_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2375DWZC/",
"accession": "IGVFFI2375DWZC",
"aliases": [
"bradley-bernstein:SS-LS_2261_R2",
"buenrostro-bernstein:SS-LS_2261_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:45:15.572501+00:00",
"file_format": "fastq",
"file_size": 940134957,
"href": "/sequence-files/IGVFFI2375DWZC/@@download/IGVFFI2375DWZC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/47797f16-3217-4665-9f7f-e2c4471ff95e/IGVFFI2375DWZC.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-25_L1_SS-PKR-3_SS-V1-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4988JVYK/",
"accession": "IGVFFI4988JVYK",
"aliases": [
"bradley-bernstein:SS-LS_2357_R1",
"buenrostro-bernstein:SS-LS_2357_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:52:39.391243+00:00",
"file_format": "fastq",
"file_size": 551423239,
"href": "/sequence-files/IGVFFI4988JVYK/@@download/IGVFFI4988JVYK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/79f730fd-28dc-4ab8-9383-3040a0a09426/IGVFFI4988JVYK.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-25_L2_SS-PKR-3_SS-V1-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0562AOML/",
"accession": "IGVFFI0562AOML",
"aliases": [
"bradley-bernstein:SS-LS_2357_R2",
"buenrostro-bernstein:SS-LS_2357_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:52:40.559587+00:00",
"file_format": "fastq",
"file_size": 943905533,
"href": "/sequence-files/IGVFFI0562AOML/@@download/IGVFFI0562AOML.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/401ec2b0-a8c0-4088-b639-a5fe87f2f439/IGVFFI0562AOML.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-25_L2_SS-PKR-3_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/IGVFDS7919DUHD/",
"accession": "IGVFDS7919DUHD",
"status": "released"
}
],
"release_timestamp": "2025-01-14T19:11:19.325341+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM6852UYUG/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6852UYUG",
"aliases": [
"bradley-bernstein:BioSam 4563_SS-PKR 3",
"buenrostro-bernstein:BioSam 4563_SS-PKR 3"
],
"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 3), 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": "2024-02-12T21:23:26.123062+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "a5354671-f8ce-40eb-8e06-61e678352aed"
}