{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4146ZPMG/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4146ZPMG",
"aliases": [
"bradley-bernstein:scATAC Lib 33",
"buenrostro-bernstein:scATAC Lib 33"
],
"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 [IGVFSM8281LNKR](/primary-cells/IGVFSM8281LNKR/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/primary-cells/IGVFSM8281LNKR/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4146ZPMG](/measurement-sets/IGVFDS4146ZPMG/) has sequence file(s): [IGVFFI3816LCGO](/sequence-files/IGVFFI3816LCGO/), [IGVFFI2164CTBT](/sequence-files/IGVFFI2164CTBT/), [IGVFFI1866KFSL](/sequence-files/IGVFFI1866KFSL/), [IGVFFI3472ZOIB](/sequence-files/IGVFFI3472ZOIB/), [IGVFFI8818ZVGY](/sequence-files/IGVFFI8818ZVGY/), [IGVFFI0332ZZVZ](/sequence-files/IGVFFI0332ZZVZ/), [IGVFFI7056KOLF](/sequence-files/IGVFFI7056KOLF/), [IGVFFI1981ZXEQ](/sequence-files/IGVFFI1981ZXEQ/), [IGVFFI7921ZPQB](/sequence-files/IGVFFI7921ZPQB/), [IGVFFI1168JFXY](/sequence-files/IGVFFI1168JFXY/), [IGVFFI5099ZFAG](/sequence-files/IGVFFI5099ZFAG/), [IGVFFI5074NNTF](/sequence-files/IGVFFI5074NNTF/), [IGVFFI1399QXKT](/sequence-files/IGVFFI1399QXKT/), [IGVFFI5362PVOG](/sequence-files/IGVFFI5362PVOG/), [IGVFFI1716CNEA](/sequence-files/IGVFFI1716CNEA/), [IGVFFI8600PXRN](/sequence-files/IGVFFI8600PXRN/) 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/IGVFDS4146ZPMG/"
}
],
"WARNING": [
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS4146ZPMG](/measurement-sets/IGVFDS4146ZPMG/) 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/IGVFDS4146ZPMG/"
}
]
},
"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": "2024-02-12T21:12:46.459238+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO2457AMDL/",
"accession": "IGVFDO2457AMDL",
"aliases": [
"bradley-bernstein:Donor 1509",
"buenrostro-bernstein:Donor 1509"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI3816LCGO/",
"accession": "IGVFFI3816LCGO",
"aliases": [
"bradley-bernstein:SS-LS_2301_R1",
"buenrostro-bernstein:SS-LS_2301_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:33:41.547762+00:00",
"file_format": "fastq",
"file_size": 371796968,
"href": "/sequence-files/IGVFFI3816LCGO/@@download/IGVFFI3816LCGO.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/d43da8b2-dd3d-4b8b-ab0a-ea5a53c86ed6/IGVFFI3816LCGO.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-65_L1_SS-PKR-6_SS-V1-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2164CTBT/",
"accession": "IGVFFI2164CTBT",
"aliases": [
"bradley-bernstein:SS-LS_2301_R2",
"buenrostro-bernstein:SS-LS_2301_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:33:42.780110+00:00",
"file_format": "fastq",
"file_size": 638304126,
"href": "/sequence-files/IGVFFI2164CTBT/@@download/IGVFFI2164CTBT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/0cc93009-9eec-4adb-ae25-611a6cb8e7ae/IGVFFI2164CTBT.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-65_L1_SS-PKR-6_SS-V1-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1866KFSL/",
"accession": "IGVFFI1866KFSL",
"aliases": [
"bradley-bernstein:SS-LS_1727_R1",
"buenrostro-bernstein:SS-LS_1727_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:33:02.221086+00:00",
"file_format": "fastq",
"file_size": 37981,
"href": "/sequence-files/IGVFFI1866KFSL/@@download/IGVFFI1866KFSL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/75fa961f-9315-4b01-9487-e0860fe55da2/IGVFFI1866KFSL.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-1128_L4_SS-PKR-6_SS-V1-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3472ZOIB/",
"accession": "IGVFFI3472ZOIB",
"aliases": [
"bradley-bernstein:SS-LS_1535_R1",
"buenrostro-bernstein:SS-LS_1535_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:31:25.808610+00:00",
"file_format": "fastq",
"file_size": 39609,
"href": "/sequence-files/IGVFFI3472ZOIB/@@download/IGVFFI3472ZOIB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/3d11876b-3cd9-42bf-863f-c05229fb8126/IGVFFI3472ZOIB.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-1128_L2_SS-PKR-6_SS-V1-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8818ZVGY/",
"accession": "IGVFFI8818ZVGY",
"aliases": [
"bradley-bernstein:SS-LS_1439_R1",
"buenrostro-bernstein:SS-LS_1439_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:30:46.164927+00:00",
"file_format": "fastq",
"file_size": 37275,
"href": "/sequence-files/IGVFFI8818ZVGY/@@download/IGVFFI8818ZVGY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/e6b26790-c097-4e9e-80f6-e205e347dff1/IGVFFI8818ZVGY.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-1128_L1_SS-PKR-6_SS-V1-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0332ZZVZ/",
"accession": "IGVFFI0332ZZVZ",
"aliases": [
"bradley-bernstein:SS-LS_1439_R2",
"buenrostro-bernstein:SS-LS_1439_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:30:47.580340+00:00",
"file_format": "fastq",
"file_size": 79623,
"href": "/sequence-files/IGVFFI0332ZZVZ/@@download/IGVFFI0332ZZVZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/4a053485-cded-4284-9ef3-6095a1cc5637/IGVFFI0332ZZVZ.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-1128_L1_SS-PKR-6_SS-V1-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7056KOLF/",
"accession": "IGVFFI7056KOLF",
"aliases": [
"bradley-bernstein:SS-LS_1631_R1",
"buenrostro-bernstein:SS-LS_1631_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:32:00.540028+00:00",
"file_format": "fastq",
"file_size": 35482,
"href": "/sequence-files/IGVFFI7056KOLF/@@download/IGVFFI7056KOLF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/647de6d4-0ccd-422f-be72-977b54623964/IGVFFI7056KOLF.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-1128_L3_SS-PKR-6_SS-V1-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1981ZXEQ/",
"accession": "IGVFFI1981ZXEQ",
"aliases": [
"bradley-bernstein:SS-LS_1631_R2",
"buenrostro-bernstein:SS-LS_1631_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:32:01.499430+00:00",
"file_format": "fastq",
"file_size": 76191,
"href": "/sequence-files/IGVFFI1981ZXEQ/@@download/IGVFFI1981ZXEQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/89a92abd-7019-4c1a-9e0c-388e3c4d5a96/IGVFFI1981ZXEQ.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-1128_L3_SS-PKR-6_SS-V1-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7921ZPQB/",
"accession": "IGVFFI7921ZPQB",
"aliases": [
"bradley-bernstein:SS-LS_1535_R2",
"buenrostro-bernstein:SS-LS_1535_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:31:26.706798+00:00",
"file_format": "fastq",
"file_size": 84909,
"href": "/sequence-files/IGVFFI7921ZPQB/@@download/IGVFFI7921ZPQB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/e217f7fb-51d8-4587-a45f-3773a2f86754/IGVFFI7921ZPQB.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-1128_L2_SS-PKR-6_SS-V1-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1168JFXY/",
"accession": "IGVFFI1168JFXY",
"aliases": [
"bradley-bernstein:SS-LS_2397_R1",
"buenrostro-bernstein:SS-LS_2397_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:34:18.378775+00:00",
"file_format": "fastq",
"file_size": 374355354,
"href": "/sequence-files/IGVFFI1168JFXY/@@download/IGVFFI1168JFXY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/e2facbda-bb89-46e6-868c-675f742c4048/IGVFFI1168JFXY.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-65_L2_SS-PKR-6_SS-V1-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5099ZFAG/",
"accession": "IGVFFI5099ZFAG",
"aliases": [
"bradley-bernstein:SS-LS_2397_R2",
"buenrostro-bernstein:SS-LS_2397_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:34:19.446918+00:00",
"file_format": "fastq",
"file_size": 642332867,
"href": "/sequence-files/IGVFFI5099ZFAG/@@download/IGVFFI5099ZFAG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/2c592e08-0d30-449d-b751-2223febfc888/IGVFFI5099ZFAG.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-65_L2_SS-PKR-6_SS-V1-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5074NNTF/",
"accession": "IGVFFI5074NNTF",
"aliases": [
"bradley-bernstein:SS-LS_2493_R1",
"buenrostro-bernstein:SS-LS_2493_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:34:56.501339+00:00",
"file_format": "fastq",
"file_size": 372386751,
"href": "/sequence-files/IGVFFI5074NNTF/@@download/IGVFFI5074NNTF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/b402dd88-3bc7-4901-9763-308166aa9d53/IGVFFI5074NNTF.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-65_L3_SS-PKR-6_SS-V1-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1399QXKT/",
"accession": "IGVFFI1399QXKT",
"aliases": [
"bradley-bernstein:SS-LS_1727_R2",
"buenrostro-bernstein:SS-LS_1727_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:33:03.121911+00:00",
"file_format": "fastq",
"file_size": 82119,
"href": "/sequence-files/IGVFFI1399QXKT/@@download/IGVFFI1399QXKT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/053af528-3f44-4644-9a41-ec49230dec60/IGVFFI1399QXKT.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-1128_L4_SS-PKR-6_SS-V1-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5362PVOG/",
"accession": "IGVFFI5362PVOG",
"aliases": [
"bradley-bernstein:SS-LS_2493_R2",
"buenrostro-bernstein:SS-LS_2493_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:34:57.403431+00:00",
"file_format": "fastq",
"file_size": 637649885,
"href": "/sequence-files/IGVFFI5362PVOG/@@download/IGVFFI5362PVOG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/c15f2870-3a76-4ee3-ac69-14c27c52a7dc/IGVFFI5362PVOG.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-65_L3_SS-PKR-6_SS-V1-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1716CNEA/",
"accession": "IGVFFI1716CNEA",
"aliases": [
"bradley-bernstein:SS-LS_2589_R1",
"buenrostro-bernstein:SS-LS_2589_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:35:30.707742+00:00",
"file_format": "fastq",
"file_size": 370332785,
"href": "/sequence-files/IGVFFI1716CNEA/@@download/IGVFFI1716CNEA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/937d7081-7f90-4b18-8c84-0afe49de190b/IGVFFI1716CNEA.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-65_L4_SS-PKR-6_SS-V1-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8600PXRN/",
"accession": "IGVFFI8600PXRN",
"aliases": [
"bradley-bernstein:SS-LS_2589_R2",
"buenrostro-bernstein:SS-LS_2589_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:35:31.635721+00:00",
"file_format": "fastq",
"file_size": 635986552,
"href": "/sequence-files/IGVFFI8600PXRN/@@download/IGVFFI8600PXRN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/02/12/57c12efe-7078-432a-a982-058728e7dc35/IGVFFI8600PXRN.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-65_L4_SS-PKR-6_SS-V1-3rd-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/IGVFDS3398OXZV/",
"accession": "IGVFDS3398OXZV",
"status": "released"
}
],
"release_timestamp": "2025-01-14T19:17:42.120352+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM8281LNKR/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8281LNKR",
"aliases": [
"bradley-bernstein:BioSam 4565_SS-PKR 6",
"buenrostro-bernstein:BioSam 4565_SS-PKR 6"
],
"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 6), 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": "2024-02-12T21:30:46.164927+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "d5afe9c5-e0be-4f1e-b542-0908bd2f396b"
}