{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4563BCFV/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4563BCFV",
"aliases": [
"bradley-bernstein:scATAC Lib 3",
"buenrostro-bernstein:scATAC Lib 3"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002764/",
"assay_slims": [
"chromatin accessibility"
],
"status": "released",
"term_name": "single-cell ATAC-seq"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS4563BCFV](/measurement-sets/IGVFDS4563BCFV/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_file_set_missing_publication",
"path": "/measurement-sets/IGVFDS4563BCFV/"
},
{
"category": "mismatched status",
"detail": "Released primary cell [IGVFSM2806AZKY](/primary-cells/IGVFSM2806AZKY/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/primary-cells/IGVFSM2806AZKY/"
},
{
"category": "missing publication",
"detail": "Primary cell [IGVFSM2806AZKY](/primary-cells/IGVFSM2806AZKY/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_sample_missing_publication",
"path": "/primary-cells/IGVFSM2806AZKY/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4563BCFV](/measurement-sets/IGVFDS4563BCFV/) has sequence file(s): [IGVFFI3954GPMB](/sequence-files/IGVFFI3954GPMB/), [IGVFFI3957JOPX](/sequence-files/IGVFFI3957JOPX/), [IGVFFI3892XYMG](/sequence-files/IGVFFI3892XYMG/), [IGVFFI1871NJSS](/sequence-files/IGVFFI1871NJSS/), [IGVFFI4176XIYD](/sequence-files/IGVFFI4176XIYD/), [IGVFFI5362BWPF](/sequence-files/IGVFFI5362BWPF/), [IGVFFI5565HNNE](/sequence-files/IGVFFI5565HNNE/), [IGVFFI9825AUKB](/sequence-files/IGVFFI9825AUKB/), [IGVFFI6058LULB](/sequence-files/IGVFFI6058LULB/), [IGVFFI9491DCWA](/sequence-files/IGVFFI9491DCWA/), [IGVFFI5273FKIT](/sequence-files/IGVFFI5273FKIT/), [IGVFFI3201HPKG](/sequence-files/IGVFFI3201HPKG/), [IGVFFI2695NJNM](/sequence-files/IGVFFI2695NJNM/), [IGVFFI8222QCNL](/sequence-files/IGVFFI8222QCNL/), [IGVFFI6596NRFO](/sequence-files/IGVFFI6596NRFO/), [IGVFFI7363XROA](/sequence-files/IGVFFI7363XROA/) which do not have any `seqspecs`. Sequence files in a file set associated with single cell data are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS4563BCFV/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4563BCFV](/measurement-sets/IGVFDS4563BCFV/) has a sequence file [IGVFFI3954GPMB](/sequence-files/IGVFFI3954GPMB/) missing `read_names`. Sequence files are expected to have read names.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_single_cell_read_names",
"path": "/measurement-sets/IGVFDS4563BCFV/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4563BCFV](/measurement-sets/IGVFDS4563BCFV/) has a sequence file [IGVFFI3957JOPX](/sequence-files/IGVFFI3957JOPX/) missing `read_names`. Sequence files are expected to have read names.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_single_cell_read_names",
"path": "/measurement-sets/IGVFDS4563BCFV/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4563BCFV](/measurement-sets/IGVFDS4563BCFV/) has a sequence file [IGVFFI3892XYMG](/sequence-files/IGVFFI3892XYMG/) missing `read_names`. Sequence files are expected to have read names.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_single_cell_read_names",
"path": "/measurement-sets/IGVFDS4563BCFV/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4563BCFV](/measurement-sets/IGVFDS4563BCFV/) has a sequence file [IGVFFI1871NJSS](/sequence-files/IGVFFI1871NJSS/) missing `read_names`. Sequence files are expected to have read names.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_single_cell_read_names",
"path": "/measurement-sets/IGVFDS4563BCFV/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4563BCFV](/measurement-sets/IGVFDS4563BCFV/) has a sequence file [IGVFFI4176XIYD](/sequence-files/IGVFFI4176XIYD/) missing `read_names`. Sequence files are expected to have read names.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_single_cell_read_names",
"path": "/measurement-sets/IGVFDS4563BCFV/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4563BCFV](/measurement-sets/IGVFDS4563BCFV/) has a sequence file [IGVFFI5362BWPF](/sequence-files/IGVFFI5362BWPF/) missing `read_names`. Sequence files are expected to have read names.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_single_cell_read_names",
"path": "/measurement-sets/IGVFDS4563BCFV/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4563BCFV](/measurement-sets/IGVFDS4563BCFV/) has a sequence file [IGVFFI5565HNNE](/sequence-files/IGVFFI5565HNNE/) missing `read_names`. Sequence files are expected to have read names.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_single_cell_read_names",
"path": "/measurement-sets/IGVFDS4563BCFV/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4563BCFV](/measurement-sets/IGVFDS4563BCFV/) has a sequence file [IGVFFI9825AUKB](/sequence-files/IGVFFI9825AUKB/) missing `read_names`. Sequence files are expected to have read names.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_single_cell_read_names",
"path": "/measurement-sets/IGVFDS4563BCFV/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4563BCFV](/measurement-sets/IGVFDS4563BCFV/) has a sequence file [IGVFFI6058LULB](/sequence-files/IGVFFI6058LULB/) missing `read_names`. Sequence files are expected to have read names.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_single_cell_read_names",
"path": "/measurement-sets/IGVFDS4563BCFV/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4563BCFV](/measurement-sets/IGVFDS4563BCFV/) has a sequence file [IGVFFI9491DCWA](/sequence-files/IGVFFI9491DCWA/) missing `read_names`. Sequence files are expected to have read names.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_single_cell_read_names",
"path": "/measurement-sets/IGVFDS4563BCFV/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4563BCFV](/measurement-sets/IGVFDS4563BCFV/) has a sequence file [IGVFFI5273FKIT](/sequence-files/IGVFFI5273FKIT/) missing `read_names`. Sequence files are expected to have read names.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_single_cell_read_names",
"path": "/measurement-sets/IGVFDS4563BCFV/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4563BCFV](/measurement-sets/IGVFDS4563BCFV/) has a sequence file [IGVFFI3201HPKG](/sequence-files/IGVFFI3201HPKG/) missing `read_names`. Sequence files are expected to have read names.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_single_cell_read_names",
"path": "/measurement-sets/IGVFDS4563BCFV/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4563BCFV](/measurement-sets/IGVFDS4563BCFV/) has a sequence file [IGVFFI2695NJNM](/sequence-files/IGVFFI2695NJNM/) missing `read_names`. Sequence files are expected to have read names.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_single_cell_read_names",
"path": "/measurement-sets/IGVFDS4563BCFV/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4563BCFV](/measurement-sets/IGVFDS4563BCFV/) has a sequence file [IGVFFI8222QCNL](/sequence-files/IGVFFI8222QCNL/) missing `read_names`. Sequence files are expected to have read names.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_single_cell_read_names",
"path": "/measurement-sets/IGVFDS4563BCFV/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4563BCFV](/measurement-sets/IGVFDS4563BCFV/) has a sequence file [IGVFFI6596NRFO](/sequence-files/IGVFFI6596NRFO/) missing `read_names`. Sequence files are expected to have read names.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_single_cell_read_names",
"path": "/measurement-sets/IGVFDS4563BCFV/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4563BCFV](/measurement-sets/IGVFDS4563BCFV/) has a sequence file [IGVFFI7363XROA](/sequence-files/IGVFFI7363XROA/) missing `read_names`. Sequence files are expected to have read names.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_single_cell_read_names",
"path": "/measurement-sets/IGVFDS4563BCFV/"
},
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS4563BCFV](/measurement-sets/IGVFDS4563BCFV/) is missing required `strand_specificity`. Single-cell assays are expected to specify strand specificity.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_strand_specificity",
"path": "/measurement-sets/IGVFDS4563BCFV/"
},
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS4563BCFV](/measurement-sets/IGVFDS4563BCFV/) 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": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_onlist",
"path": "/measurement-sets/IGVFDS4563BCFV/"
}
]
},
"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": [],
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:12:40.192886+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"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/IGVFFI3954GPMB/",
"accession": "IGVFFI3954GPMB",
"aliases": [
"bradley-bernstein:SS-LS_1571_R1",
"buenrostro-bernstein:SS-LS_1571_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:31:37.696074+00:00",
"file_format": "fastq",
"file_size": 97555,
"href": "/sequence-files/IGVFFI3954GPMB/@@download/IGVFFI3954GPMB.fastq.gz",
"md5sum": "13d0b84a6c5e3ec2b4a7008c94f67995",
"s3_uri": "s3://igvf-files/2024/02/12/4ea09995-82a9-4936-89d7-f491cfab9956/IGVFFI3954GPMB.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-1068_L3_SS-PKR-1_SS-V1-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3957JOPX/",
"accession": "IGVFFI3957JOPX",
"aliases": [
"bradley-bernstein:SS-LS_1571_R2",
"buenrostro-bernstein:SS-LS_1571_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:31:38.930138+00:00",
"file_format": "fastq",
"file_size": 216515,
"href": "/sequence-files/IGVFFI3957JOPX/@@download/IGVFFI3957JOPX.fastq.gz",
"md5sum": "7b5eede8111dbd13fccf0b63edcd0ddf",
"s3_uri": "s3://igvf-files/2024/02/12/6820df9c-a04a-4b2e-8da5-3603953c7a05/IGVFFI3957JOPX.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-1068_L3_SS-PKR-1_SS-V1-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3892XYMG/",
"accession": "IGVFFI3892XYMG",
"aliases": [
"bradley-bernstein:SS-LS_1379_R1",
"buenrostro-bernstein:SS-LS_1379_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:30:24.060654+00:00",
"file_format": "fastq",
"file_size": 89093,
"href": "/sequence-files/IGVFFI3892XYMG/@@download/IGVFFI3892XYMG.fastq.gz",
"md5sum": "49a97b6ca24e4afdfeec10ae85088d02",
"s3_uri": "s3://igvf-files/2024/02/12/b282d767-ba8c-4bb4-b952-4b37357f603e/IGVFFI3892XYMG.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-1068_L1_SS-PKR-1_SS-V1-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1871NJSS/",
"accession": "IGVFFI1871NJSS",
"aliases": [
"bradley-bernstein:SS-LS_1379_R2",
"buenrostro-bernstein:SS-LS_1379_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:30:24.949761+00:00",
"file_format": "fastq",
"file_size": 195675,
"href": "/sequence-files/IGVFFI1871NJSS/@@download/IGVFFI1871NJSS.fastq.gz",
"md5sum": "20399b2cc468bdadbdbb14cfedbd9c3c",
"s3_uri": "s3://igvf-files/2024/02/12/43a96eb4-4ca0-4029-b226-d702a087636f/IGVFFI1871NJSS.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-1068_L1_SS-PKR-1_SS-V1-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4176XIYD/",
"accession": "IGVFFI4176XIYD",
"aliases": [
"bradley-bernstein:SS-LS_1667_R1",
"buenrostro-bernstein:SS-LS_1667_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:32:38.051194+00:00",
"file_format": "fastq",
"file_size": 73917,
"href": "/sequence-files/IGVFFI4176XIYD/@@download/IGVFFI4176XIYD.fastq.gz",
"md5sum": "a125cf57edbb60c48f32c4854b3771e1",
"s3_uri": "s3://igvf-files/2024/02/12/971d3139-af96-48ca-8a1d-09da9121858c/IGVFFI4176XIYD.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-1068_L4_SS-PKR-1_SS-V1-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5362BWPF/",
"accession": "IGVFFI5362BWPF",
"aliases": [
"bradley-bernstein:SS-LS_2337_R2",
"buenrostro-bernstein:SS-LS_2337_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:33:56.099469+00:00",
"file_format": "fastq",
"file_size": 1771233488,
"href": "/sequence-files/IGVFFI5362BWPF/@@download/IGVFFI5362BWPF.fastq.gz",
"md5sum": "e970a8d31ddd609c6873e1ffe9501455",
"s3_uri": "s3://igvf-files/2024/02/12/6bc3f64f-02fd-4834-bd74-1dd87e3ab01f/IGVFFI5362BWPF.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-5_L2_SS-PKR-1_SS-V1-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5565HNNE/",
"accession": "IGVFFI5565HNNE",
"aliases": [
"bradley-bernstein:SS-LS_2241_R2",
"buenrostro-bernstein:SS-LS_2241_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:33:18.915316+00:00",
"file_format": "fastq",
"file_size": 1765118003,
"href": "/sequence-files/IGVFFI5565HNNE/@@download/IGVFFI5565HNNE.fastq.gz",
"md5sum": "9b9e3306c97dc3f6fa48fd03b25968de",
"s3_uri": "s3://igvf-files/2024/02/12/3aba8fae-42dc-48b5-95c2-0132eca06e2b/IGVFFI5565HNNE.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-5_L1_SS-PKR-1_SS-V1-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9825AUKB/",
"accession": "IGVFFI9825AUKB",
"aliases": [
"bradley-bernstein:SS-LS_1475_R1",
"buenrostro-bernstein:SS-LS_1475_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:31:02.600335+00:00",
"file_format": "fastq",
"file_size": 85919,
"href": "/sequence-files/IGVFFI9825AUKB/@@download/IGVFFI9825AUKB.fastq.gz",
"md5sum": "ade475a7b1144c170ea77183b5e9f4a8",
"s3_uri": "s3://igvf-files/2024/02/12/e8a1620d-dbe9-47c0-9fa6-70228145ac67/IGVFFI9825AUKB.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-1068_L2_SS-PKR-1_SS-V1-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6058LULB/",
"accession": "IGVFFI6058LULB",
"aliases": [
"bradley-bernstein:SS-LS_1475_R2",
"buenrostro-bernstein:SS-LS_1475_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:31:03.494220+00:00",
"file_format": "fastq",
"file_size": 187861,
"href": "/sequence-files/IGVFFI6058LULB/@@download/IGVFFI6058LULB.fastq.gz",
"md5sum": "24e9b652e7eba76c9f14c54a7de72d7f",
"s3_uri": "s3://igvf-files/2024/02/12/9ea573e4-6036-4e55-aae3-5b1fdf52f3ed/IGVFFI6058LULB.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-1068_L2_SS-PKR-1_SS-V1-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9491DCWA/",
"accession": "IGVFFI9491DCWA",
"aliases": [
"bradley-bernstein:SS-LS_1667_R2",
"buenrostro-bernstein:SS-LS_1667_R2"
],
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