{
"@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/",
"assay_slims": [
"chromatin accessibility"
],
"status": "released",
"term_name": "single-cell ATAC-seq"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS4146ZPMG](/measurement-sets/IGVFDS4146ZPMG/) 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/IGVFDS4146ZPMG/"
},
{
"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 publication",
"detail": "Primary cell [IGVFSM8281LNKR](/primary-cells/IGVFSM8281LNKR/) 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/IGVFSM8281LNKR/"
}
],
"NOT_COMPLIANT": [
{
"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 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/IGVFDS4146ZPMG/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4146ZPMG](/measurement-sets/IGVFDS4146ZPMG/) has a sequence file [IGVFFI3816LCGO](/sequence-files/IGVFFI3816LCGO/) 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/IGVFDS4146ZPMG/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4146ZPMG](/measurement-sets/IGVFDS4146ZPMG/) has a sequence file [IGVFFI2164CTBT](/sequence-files/IGVFFI2164CTBT/) 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/IGVFDS4146ZPMG/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4146ZPMG](/measurement-sets/IGVFDS4146ZPMG/) has a sequence file [IGVFFI1866KFSL](/sequence-files/IGVFFI1866KFSL/) 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/IGVFDS4146ZPMG/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4146ZPMG](/measurement-sets/IGVFDS4146ZPMG/) has a sequence file [IGVFFI3472ZOIB](/sequence-files/IGVFFI3472ZOIB/) 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/IGVFDS4146ZPMG/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4146ZPMG](/measurement-sets/IGVFDS4146ZPMG/) has a sequence file [IGVFFI8818ZVGY](/sequence-files/IGVFFI8818ZVGY/) 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/IGVFDS4146ZPMG/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4146ZPMG](/measurement-sets/IGVFDS4146ZPMG/) has a sequence file [IGVFFI0332ZZVZ](/sequence-files/IGVFFI0332ZZVZ/) 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/IGVFDS4146ZPMG/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4146ZPMG](/measurement-sets/IGVFDS4146ZPMG/) has a sequence file [IGVFFI7056KOLF](/sequence-files/IGVFFI7056KOLF/) 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/IGVFDS4146ZPMG/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4146ZPMG](/measurement-sets/IGVFDS4146ZPMG/) has a sequence file [IGVFFI1981ZXEQ](/sequence-files/IGVFFI1981ZXEQ/) 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/IGVFDS4146ZPMG/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4146ZPMG](/measurement-sets/IGVFDS4146ZPMG/) has a sequence file [IGVFFI7921ZPQB](/sequence-files/IGVFFI7921ZPQB/) 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/IGVFDS4146ZPMG/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4146ZPMG](/measurement-sets/IGVFDS4146ZPMG/) has a sequence file [IGVFFI1168JFXY](/sequence-files/IGVFFI1168JFXY/) 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/IGVFDS4146ZPMG/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4146ZPMG](/measurement-sets/IGVFDS4146ZPMG/) has a sequence file [IGVFFI5099ZFAG](/sequence-files/IGVFFI5099ZFAG/) 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/IGVFDS4146ZPMG/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4146ZPMG](/measurement-sets/IGVFDS4146ZPMG/) has a sequence file [IGVFFI5074NNTF](/sequence-files/IGVFFI5074NNTF/) 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/IGVFDS4146ZPMG/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4146ZPMG](/measurement-sets/IGVFDS4146ZPMG/) has a sequence file [IGVFFI1399QXKT](/sequence-files/IGVFFI1399QXKT/) 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/IGVFDS4146ZPMG/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4146ZPMG](/measurement-sets/IGVFDS4146ZPMG/) has a sequence file [IGVFFI5362PVOG](/sequence-files/IGVFFI5362PVOG/) 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/IGVFDS4146ZPMG/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4146ZPMG](/measurement-sets/IGVFDS4146ZPMG/) has a sequence file [IGVFFI1716CNEA](/sequence-files/IGVFFI1716CNEA/) 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/IGVFDS4146ZPMG/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS4146ZPMG](/measurement-sets/IGVFDS4146ZPMG/) has a sequence file [IGVFFI8600PXRN](/sequence-files/IGVFFI8600PXRN/) 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/IGVFDS4146ZPMG/"
},
{
"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": 50,
"level_name": "NOT_COMPLIANT",
"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": [],
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:12:46.459238+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/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",
"md5sum": "d50a4e6d26c04298f4db638888569a1d",
"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",
"md5sum": "01eff1b7e68b59d0f8681f80d9347356",
"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",
"md5sum": "82298db48c4a099e7e513abb3c921c52",
"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",
"md5sum": "37b34635e589018446ab8685cb71bbb1",
"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",
"md5sum": "1c9a128748f50846be711f9e4e80d98b",
"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",
"md5sum": "c45238f7b1ed7fc0b7f427f530696f3c",
"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",
"md5sum": "9577211ccac4d358495b8ca826124689",
"s3_uri": "s3://igvf-files/2024/02/12/647de6d4-0ccd-422f-be72-977b54623964/IGVFFI7056KOLF.fastq.gz",
"sequencing_platform": {
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"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",
"md5sum": "41195f96cecec402c0295d0bee4f64a9",
"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",
"md5sum": "549bd0d66a07d40567288114764ea0ab",
"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",
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