{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9565KMHX/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9565KMHX",
"aliases": [
"bradley-bernstein:scRNA Lib 9",
"buenrostro-bernstein:scRNA Lib 9"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002631/",
"assay_slims": [
"gene expression"
],
"status": "released",
"term_name": "single-cell RNA sequencing assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released primary cell [IGVFSM1342VWSK](/primary-cells/IGVFSM1342VWSK/) has in progress subobject source [jason-buenrostro](/sources/jason-buenrostro/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/primary-cells/IGVFSM1342VWSK/"
},
{
"category": "missing publication",
"detail": "Primary cell [IGVFSM1342VWSK](/primary-cells/IGVFSM1342VWSK/) 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/IGVFSM1342VWSK/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS9565KMHX](/measurement-sets/IGVFDS9565KMHX/) 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/IGVFDS9565KMHX/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9565KMHX](/measurement-sets/IGVFDS9565KMHX/) has sequence file(s): [IGVFFI7222CDWH](/sequence-files/IGVFFI7222CDWH/), [IGVFFI4839ZQIM](/sequence-files/IGVFFI4839ZQIM/), [IGVFFI9383XMBO](/sequence-files/IGVFFI9383XMBO/), [IGVFFI5540MPSN](/sequence-files/IGVFFI5540MPSN/), [IGVFFI7156TUMO](/sequence-files/IGVFFI7156TUMO/), [IGVFFI6140GLNG](/sequence-files/IGVFFI6140GLNG/), [IGVFFI3824BDUB](/sequence-files/IGVFFI3824BDUB/), [IGVFFI5738HJOJ](/sequence-files/IGVFFI5738HJOJ/), [IGVFFI6697AIGY](/sequence-files/IGVFFI6697AIGY/), [IGVFFI1282VFDG](/sequence-files/IGVFFI1282VFDG/), [IGVFFI7801UGMQ](/sequence-files/IGVFFI7801UGMQ/), [IGVFFI6021QDUP](/sequence-files/IGVFFI6021QDUP/), [IGVFFI8338SFGQ](/sequence-files/IGVFFI8338SFGQ/), [IGVFFI7372YKSL](/sequence-files/IGVFFI7372YKSL/), [IGVFFI4718RSEL](/sequence-files/IGVFFI4718RSEL/), [IGVFFI7601XTUK](/sequence-files/IGVFFI7601XTUK/) 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/IGVFDS9565KMHX/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS9565KMHX](/measurement-sets/IGVFDS9565KMHX/) has a sequence file [IGVFFI7222CDWH](/sequence-files/IGVFFI7222CDWH/) 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/IGVFDS9565KMHX/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS9565KMHX](/measurement-sets/IGVFDS9565KMHX/) has a sequence file [IGVFFI4839ZQIM](/sequence-files/IGVFFI4839ZQIM/) 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/IGVFDS9565KMHX/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS9565KMHX](/measurement-sets/IGVFDS9565KMHX/) has a sequence file [IGVFFI9383XMBO](/sequence-files/IGVFFI9383XMBO/) 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/IGVFDS9565KMHX/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS9565KMHX](/measurement-sets/IGVFDS9565KMHX/) has a sequence file [IGVFFI5540MPSN](/sequence-files/IGVFFI5540MPSN/) 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/IGVFDS9565KMHX/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS9565KMHX](/measurement-sets/IGVFDS9565KMHX/) has a sequence file [IGVFFI7156TUMO](/sequence-files/IGVFFI7156TUMO/) 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/IGVFDS9565KMHX/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS9565KMHX](/measurement-sets/IGVFDS9565KMHX/) has a sequence file [IGVFFI6140GLNG](/sequence-files/IGVFFI6140GLNG/) 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/IGVFDS9565KMHX/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS9565KMHX](/measurement-sets/IGVFDS9565KMHX/) has a sequence file [IGVFFI3824BDUB](/sequence-files/IGVFFI3824BDUB/) 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/IGVFDS9565KMHX/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS9565KMHX](/measurement-sets/IGVFDS9565KMHX/) has a sequence file [IGVFFI5738HJOJ](/sequence-files/IGVFFI5738HJOJ/) 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/IGVFDS9565KMHX/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS9565KMHX](/measurement-sets/IGVFDS9565KMHX/) has a sequence file [IGVFFI6697AIGY](/sequence-files/IGVFFI6697AIGY/) 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/IGVFDS9565KMHX/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS9565KMHX](/measurement-sets/IGVFDS9565KMHX/) has a sequence file [IGVFFI1282VFDG](/sequence-files/IGVFFI1282VFDG/) 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/IGVFDS9565KMHX/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS9565KMHX](/measurement-sets/IGVFDS9565KMHX/) has a sequence file [IGVFFI7801UGMQ](/sequence-files/IGVFFI7801UGMQ/) 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/IGVFDS9565KMHX/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS9565KMHX](/measurement-sets/IGVFDS9565KMHX/) has a sequence file [IGVFFI6021QDUP](/sequence-files/IGVFFI6021QDUP/) 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/IGVFDS9565KMHX/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS9565KMHX](/measurement-sets/IGVFDS9565KMHX/) has a sequence file [IGVFFI8338SFGQ](/sequence-files/IGVFFI8338SFGQ/) 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/IGVFDS9565KMHX/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS9565KMHX](/measurement-sets/IGVFDS9565KMHX/) has a sequence file [IGVFFI7372YKSL](/sequence-files/IGVFFI7372YKSL/) 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/IGVFDS9565KMHX/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS9565KMHX](/measurement-sets/IGVFDS9565KMHX/) has a sequence file [IGVFFI4718RSEL](/sequence-files/IGVFFI4718RSEL/) 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/IGVFDS9565KMHX/"
},
{
"category": "missing read names",
"detail": "Measurement set [IGVFDS9565KMHX](/measurement-sets/IGVFDS9565KMHX/) has a sequence file [IGVFFI7601XTUK](/sequence-files/IGVFFI7601XTUK/) 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/IGVFDS9565KMHX/"
},
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS9565KMHX](/measurement-sets/IGVFDS9565KMHX/) 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/IGVFDS9565KMHX/"
},
{
"category": "missing barcode onlist",
"detail": "Measurement set [IGVFDS9565KMHX](/measurement-sets/IGVFDS9565KMHX/) has an `assay_term` of single-cell RNA sequencing assay 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/IGVFDS9565KMHX/"
}
]
},
"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": "2024-02-12T21:12:41.927652+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/IGVFFI7222CDWH/",
"accession": "IGVFFI7222CDWH",
"aliases": [
"bradley-bernstein:SS-LS_1392_R2",
"buenrostro-bernstein:SS-LS_1392_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:30:30.736130+00:00",
"file_format": "fastq",
"file_size": 1974832232,
"href": "/sequence-files/IGVFFI7222CDWH/@@download/IGVFFI7222CDWH.fastq.gz",
"md5sum": "b8d171570e63e0bb805e9ecda59a921f",
"s3_uri": "s3://igvf-files/2024/02/12/f4509bc0-d5e2-4c96-9eda-94f8dea732fc/IGVFFI7222CDWH.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-1081_L1_SS-PKR-2_SS-V1-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4839ZQIM/",
"accession": "IGVFFI4839ZQIM",
"aliases": [
"bradley-bernstein:SS-LS_1488_R2",
"buenrostro-bernstein:SS-LS_1488_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:31:09.278068+00:00",
"file_format": "fastq",
"file_size": 2014625549,
"href": "/sequence-files/IGVFFI4839ZQIM/@@download/IGVFFI4839ZQIM.fastq.gz",
"md5sum": "ea71ee0d4b8a867055f0b52b8c1d03f4",
"s3_uri": "s3://igvf-files/2024/02/12/f91ef097-31d5-44cf-ad7d-57032a8ca1a0/IGVFFI4839ZQIM.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-1081_L2_SS-PKR-2_SS-V1-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9383XMBO/",
"accession": "IGVFFI9383XMBO",
"aliases": [
"bradley-bernstein:SS-LS_1584_R1",
"buenrostro-bernstein:SS-LS_1584_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:31:46.102504+00:00",
"file_format": "fastq",
"file_size": 825152954,
"href": "/sequence-files/IGVFFI9383XMBO/@@download/IGVFFI9383XMBO.fastq.gz",
"md5sum": "e4cf5bc9010d5c4ddefd489e767bee6f",
"s3_uri": "s3://igvf-files/2024/02/12/e2a0e610-856f-4967-9a9b-8fee7dc2a77c/IGVFFI9383XMBO.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-1081_L3_SS-PKR-2_SS-V1-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5540MPSN/",
"accession": "IGVFFI5540MPSN",
"aliases": [
"bradley-bernstein:SS-LS_1584_R2",
"buenrostro-bernstein:SS-LS_1584_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:31:47.072477+00:00",
"file_format": "fastq",
"file_size": 1961250616,
"href": "/sequence-files/IGVFFI5540MPSN/@@download/IGVFFI5540MPSN.fastq.gz",
"md5sum": "6df7ba9987ace35a444a017a8dfe6462",
"s3_uri": "s3://igvf-files/2024/02/12/1aec30a1-b6d1-4d46-9b46-e79d0ff114aa/IGVFFI5540MPSN.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-1081_L3_SS-PKR-2_SS-V1-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7156TUMO/",
"accession": "IGVFFI7156TUMO",
"aliases": [
"bradley-bernstein:SS-LS_2350_R1",
"buenrostro-bernstein:SS-LS_2350_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:34:00.769955+00:00",
"file_format": "fastq",
"file_size": 466020915,
"href": "/sequence-files/IGVFFI7156TUMO/@@download/IGVFFI7156TUMO.fastq.gz",
"md5sum": "04f7538c629bc5ec856373a42a542956",
"s3_uri": "s3://igvf-files/2024/02/12/b56726be-67b5-4ab8-a9b5-a127c10e9a19/IGVFFI7156TUMO.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-18_L2_SS-PKR-2_SS-V1-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6140GLNG/",
"accession": "IGVFFI6140GLNG",
"aliases": [
"bradley-bernstein:SS-LS_2446_R2",
"buenrostro-bernstein:SS-LS_2446_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:34:40.639055+00:00",
"file_format": "fastq",
"file_size": 1002971108,
"href": "/sequence-files/IGVFFI6140GLNG/@@download/IGVFFI6140GLNG.fastq.gz",
"md5sum": "3c255033ee5183dfd7dcb2cfcf5eae0f",
"s3_uri": "s3://igvf-files/2024/02/12/fb914760-c3fe-4625-a76f-82d9d420a93e/IGVFFI6140GLNG.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-18_L3_SS-PKR-2_SS-V1-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3824BDUB/",
"accession": "IGVFFI3824BDUB",
"aliases": [
"bradley-bernstein:SS-LS_1392_R1",
"buenrostro-bernstein:SS-LS_1392_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:30:29.633656+00:00",
"file_format": "fastq",
"file_size": 828709721,
"href": "/sequence-files/IGVFFI3824BDUB/@@download/IGVFFI3824BDUB.fastq.gz",
"md5sum": "73289864abd6923d8758d2551cade577",
"s3_uri": "s3://igvf-files/2024/02/12/b391fd1c-dea9-4bce-bfc9-766a5850f59b/IGVFFI3824BDUB.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-1081_L1_SS-PKR-2_SS-V1-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5738HJOJ/",
"accession": "IGVFFI5738HJOJ",
"aliases": [
"bradley-bernstein:SS-LS_2350_R2",
"buenrostro-bernstein:SS-LS_2350_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:34:02.257586+00:00",
"file_format": "fastq",
"file_size": 1009645764,
"href": "/sequence-files/IGVFFI5738HJOJ/@@download/IGVFFI5738HJOJ.fastq.gz",
"md5sum": "df30844e2ed3ec145f7ff1a7f255e333",
"s3_uri": "s3://igvf-files/2024/02/12/4b8534a2-6d9f-42b0-ad2b-96c429beb882/IGVFFI5738HJOJ.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-18_L2_SS-PKR-2_SS-V1-3rd-THIRD_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6697AIGY/",
"accession": "IGVFFI6697AIGY",
"aliases": [
"bradley-bernstein:SS-LS_2254_R1",
"buenrostro-bernstein:SS-LS_2254_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-02-12T21:33:23.978845+00:00",
"file_format": "fastq",
"file_size": 464717581,
"href": "/sequence-files/IGVFFI6697AIGY/@@download/IGVFFI6697AIGY.fastq.gz",
"md5sum": "8635e9d1de743c63e5d990678497cf4c",
"s3_uri": "s3://igvf-files/2024/02/12/23d251e2-e3e5-4e1a-a60b-00f8036a67f9/IGVFFI6697AIGY.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-18_L1_SS-PKR-2_SS-V1-3rd-THIRD_R1.fastq.gz",
"upload_status": "validated"
},
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