{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5266ONOB/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5266ONOB",
"aliases": [
"bradley-bernstein:scATAC Lib 16",
"buenrostro-bernstein:scATAC Lib 16"
],
"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 [IGVFSM3750ZIQU](/primary-cells/IGVFSM3750ZIQU/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/primary-cells/IGVFSM3750ZIQU/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5266ONOB](/measurement-sets/IGVFDS5266ONOB/) has sequence file(s): [IGVFFI1088WXYD](/sequence-files/IGVFFI1088WXYD/), [IGVFFI3489NHUK](/sequence-files/IGVFFI3489NHUK/), [IGVFFI8146ULOY](/sequence-files/IGVFFI8146ULOY/), [IGVFFI4453WONR](/sequence-files/IGVFFI4453WONR/), [IGVFFI4273YBDF](/sequence-files/IGVFFI4273YBDF/), [IGVFFI5918GACB](/sequence-files/IGVFFI5918GACB/), [IGVFFI5352VDQK](/sequence-files/IGVFFI5352VDQK/), [IGVFFI2936YIVF](/sequence-files/IGVFFI2936YIVF/), [IGVFFI8228YHSF](/sequence-files/IGVFFI8228YHSF/), [IGVFFI0211HVOS](/sequence-files/IGVFFI0211HVOS/), [IGVFFI7659JIER](/sequence-files/IGVFFI7659JIER/), [IGVFFI3035UARU](/sequence-files/IGVFFI3035UARU/), [IGVFFI1903LLEZ](/sequence-files/IGVFFI1903LLEZ/), [IGVFFI7904KSEE](/sequence-files/IGVFFI7904KSEE/), [IGVFFI2954JGXR](/sequence-files/IGVFFI2954JGXR/), [IGVFFI6790HKPB](/sequence-files/IGVFFI6790HKPB/) 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/IGVFDS5266ONOB/"
}
],
"WARNING": [
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS5266ONOB](/measurement-sets/IGVFDS5266ONOB/) 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/IGVFDS5266ONOB/"
}
]
},
"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": "2024-02-12T21:12:53.255193+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO8549ATSE/",
"accession": "IGVFDO8549ATSE",
"aliases": [
"bradley-bernstein:Donor 1511",
"buenrostro-bernstein:Donor 1511"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI1088WXYD/",
"accession": "IGVFFI1088WXYD",
"aliases": [
"bradley-bernstein:SS-LS_1405_R2",
"buenrostro-bernstein:SS-LS_1405_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:35:54.060358+00:00",
"file_format": "fastq",
"file_size": 1575,
"href": "/sequence-files/IGVFFI1088WXYD/@@download/IGVFFI1088WXYD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/d4463f17-c0a2-48f6-9ed6-862afc58d991/IGVFFI1088WXYD.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-1094_L1_SS-PKR-3_SS-V2-PLATE2-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3489NHUK/",
"accession": "IGVFFI3489NHUK",
"aliases": [
"bradley-bernstein:SS-LS_1405_R1",
"buenrostro-bernstein:SS-LS_1405_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:35:53.039765+00:00",
"file_format": "fastq",
"file_size": 958,
"href": "/sequence-files/IGVFFI3489NHUK/@@download/IGVFFI3489NHUK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/0bea8be4-821e-48c1-9f20-75574b16e530/IGVFFI3489NHUK.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-1094_L1_SS-PKR-3_SS-V2-PLATE2-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8146ULOY/",
"accession": "IGVFFI8146ULOY",
"aliases": [
"bradley-bernstein:SS-LS_1501_R1",
"buenrostro-bernstein:SS-LS_1501_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:36:55.229626+00:00",
"file_format": "fastq",
"file_size": 916,
"href": "/sequence-files/IGVFFI8146ULOY/@@download/IGVFFI8146ULOY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/bdc1bc2e-1d6c-4270-8a82-9d76baf1fb9e/IGVFFI8146ULOY.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-1094_L2_SS-PKR-3_SS-V2-PLATE2-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4453WONR/",
"accession": "IGVFFI4453WONR",
"aliases": [
"bradley-bernstein:SS-LS_1501_R2",
"buenrostro-bernstein:SS-LS_1501_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:36:56.114321+00:00",
"file_format": "fastq",
"file_size": 1521,
"href": "/sequence-files/IGVFFI4453WONR/@@download/IGVFFI4453WONR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/5e5dd7b2-9cab-44a3-84cc-4d65d098a9d4/IGVFFI4453WONR.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-1094_L2_SS-PKR-3_SS-V2-PLATE2-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4273YBDF/",
"accession": "IGVFFI4273YBDF",
"aliases": [
"bradley-bernstein:SS-LS_1693_R2",
"buenrostro-bernstein:SS-LS_1693_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:38:07.587413+00:00",
"file_format": "fastq",
"file_size": 1446,
"href": "/sequence-files/IGVFFI4273YBDF/@@download/IGVFFI4273YBDF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/081e8e47-fe92-49cb-8f45-de5bbc99f1bd/IGVFFI4273YBDF.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-1094_L4_SS-PKR-3_SS-V2-PLATE2-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5918GACB/",
"accession": "IGVFFI5918GACB",
"aliases": [
"bradley-bernstein:SS-LS_2267_R2",
"buenrostro-bernstein:SS-LS_2267_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:38:43.860036+00:00",
"file_format": "fastq",
"file_size": 794485541,
"href": "/sequence-files/IGVFFI5918GACB/@@download/IGVFFI5918GACB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/52e76dac-e436-44cb-9b47-0949b8168295/IGVFFI5918GACB.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-31_L1_SS-PKR-3_SS-V2-PLATE2-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5352VDQK/",
"accession": "IGVFFI5352VDQK",
"aliases": [
"bradley-bernstein:SS-LS_1693_R1",
"buenrostro-bernstein:SS-LS_1693_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:38:06.561959+00:00",
"file_format": "fastq",
"file_size": 904,
"href": "/sequence-files/IGVFFI5352VDQK/@@download/IGVFFI5352VDQK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/f2f9bd89-b679-4101-a1d3-80a8ef63bb75/IGVFFI5352VDQK.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-1094_L4_SS-PKR-3_SS-V2-PLATE2-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2936YIVF/",
"accession": "IGVFFI2936YIVF",
"aliases": [
"bradley-bernstein:SS-LS_1597_R1",
"buenrostro-bernstein:SS-LS_1597_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:37:31.922525+00:00",
"file_format": "fastq",
"file_size": 1030,
"href": "/sequence-files/IGVFFI2936YIVF/@@download/IGVFFI2936YIVF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/ef3906cc-fdd3-4ed6-9902-7681ef878456/IGVFFI2936YIVF.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-1094_L3_SS-PKR-3_SS-V2-PLATE2-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8228YHSF/",
"accession": "IGVFFI8228YHSF",
"aliases": [
"bradley-bernstein:SS-LS_2363_R1",
"buenrostro-bernstein:SS-LS_2363_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:39:18.054468+00:00",
"file_format": "fastq",
"file_size": 459153237,
"href": "/sequence-files/IGVFFI8228YHSF/@@download/IGVFFI8228YHSF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/a3f24f8c-3b22-4ee1-975a-dfe1e43a0f2f/IGVFFI8228YHSF.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-31_L2_SS-PKR-3_SS-V2-PLATE2-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0211HVOS/",
"accession": "IGVFFI0211HVOS",
"aliases": [
"bradley-bernstein:SS-LS_2459_R1",
"buenrostro-bernstein:SS-LS_2459_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:39:55.348092+00:00",
"file_format": "fastq",
"file_size": 457927246,
"href": "/sequence-files/IGVFFI0211HVOS/@@download/IGVFFI0211HVOS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/5c98938b-8a0d-49a6-91d0-58551949a3f0/IGVFFI0211HVOS.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-31_L3_SS-PKR-3_SS-V2-PLATE2-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7659JIER/",
"accession": "IGVFFI7659JIER",
"aliases": [
"bradley-bernstein:SS-LS_1597_R2",
"buenrostro-bernstein:SS-LS_1597_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:37:32.885105+00:00",
"file_format": "fastq",
"file_size": 1707,
"href": "/sequence-files/IGVFFI7659JIER/@@download/IGVFFI7659JIER.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/dc2123bd-bfc9-466d-b935-66e9355dd314/IGVFFI7659JIER.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-1094_L3_SS-PKR-3_SS-V2-PLATE2-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3035UARU/",
"accession": "IGVFFI3035UARU",
"aliases": [
"bradley-bernstein:SS-LS_2267_R1",
"buenrostro-bernstein:SS-LS_2267_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:38:42.920277+00:00",
"file_format": "fastq",
"file_size": 456589300,
"href": "/sequence-files/IGVFFI3035UARU/@@download/IGVFFI3035UARU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/6039927a-d887-4ce3-8f72-fd81d3544759/IGVFFI3035UARU.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-31_L1_SS-PKR-3_SS-V2-PLATE2-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1903LLEZ/",
"accession": "IGVFFI1903LLEZ",
"aliases": [
"bradley-bernstein:SS-LS_2555_R1",
"buenrostro-bernstein:SS-LS_2555_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:40:59.522740+00:00",
"file_format": "fastq",
"file_size": 454191796,
"href": "/sequence-files/IGVFFI1903LLEZ/@@download/IGVFFI1903LLEZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/8b019075-6735-48d1-b911-d1697664a77e/IGVFFI1903LLEZ.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-31_L4_SS-PKR-3_SS-V2-PLATE2-1st-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7904KSEE/",
"accession": "IGVFFI7904KSEE",
"aliases": [
"bradley-bernstein:SS-LS_2363_R2",
"buenrostro-bernstein:SS-LS_2363_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:39:18.955723+00:00",
"file_format": "fastq",
"file_size": 797854993,
"href": "/sequence-files/IGVFFI7904KSEE/@@download/IGVFFI7904KSEE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/f81339a1-8709-4c67-8a83-829f58556f17/IGVFFI7904KSEE.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-31_L2_SS-PKR-3_SS-V2-PLATE2-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2954JGXR/",
"accession": "IGVFFI2954JGXR",
"aliases": [
"bradley-bernstein:SS-LS_2555_R2",
"buenrostro-bernstein:SS-LS_2555_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:41:00.763247+00:00",
"file_format": "fastq",
"file_size": 789929635,
"href": "/sequence-files/IGVFFI2954JGXR/@@download/IGVFFI2954JGXR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/68755050-be7e-4918-bc95-eacd01efc63e/IGVFFI2954JGXR.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-31_L4_SS-PKR-3_SS-V2-PLATE2-1st-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6790HKPB/",
"accession": "IGVFFI6790HKPB",
"aliases": [
"bradley-bernstein:SS-LS_2459_R2",
"buenrostro-bernstein:SS-LS_2459_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:39:56.363434+00:00",
"file_format": "fastq",
"file_size": 793980258,
"href": "/sequence-files/IGVFFI6790HKPB/@@download/IGVFFI6790HKPB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/eb224f9b-35f6-4059-8b64-f172395b776c/IGVFFI6790HKPB.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-31_L3_SS-PKR-3_SS-V2-PLATE2-1st-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/IGVFDS7133CHRI/",
"accession": "IGVFDS7133CHRI",
"status": "released"
}
],
"release_timestamp": "2025-01-14T19:35:23.555778+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM3750ZIQU/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3750ZIQU",
"aliases": [
"bradley-bernstein:BioSam 4566_SS-PKR 3",
"buenrostro-bernstein:BioSam 4566_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 (49 years)",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2024-02-12T21:35:53.039765+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "3bbb59e7-eee3-404c-961d-f477cdc366bf"
}