{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7733OTCA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7733OTCA",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_LW279"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003660/",
"status": "released",
"term_name": "in vitro CRISPR screen using single-cell RNA-seq"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS7027VRZT](/auxiliary-sets/IGVFDS7027VRZT/) has sequence file(s) [IGVFFI1430HEKM](/sequence-files/IGVFFI1430HEKM/), [IGVFFI9545FKJR](/sequence-files/IGVFFI9545FKJR/), [IGVFFI8807NJZP](/sequence-files/IGVFFI8807NJZP/), [IGVFFI9254UKTW](/sequence-files/IGVFFI9254UKTW/), [IGVFFI1865XZZP](/sequence-files/IGVFFI1865XZZP/), [IGVFFI9553XEEI](/sequence-files/IGVFFI9553XEEI/), [IGVFFI8178OKCW](/sequence-files/IGVFFI8178OKCW/), [IGVFFI2898JUNF](/sequence-files/IGVFFI2898JUNF/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS7027VRZT/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS7027VRZT](/auxiliary-sets/IGVFDS7027VRZT/) has sequence file(s): [IGVFFI1430HEKM](/sequence-files/IGVFFI1430HEKM/), [IGVFFI9545FKJR](/sequence-files/IGVFFI9545FKJR/), [IGVFFI8807NJZP](/sequence-files/IGVFFI8807NJZP/), [IGVFFI9254UKTW](/sequence-files/IGVFFI9254UKTW/), [IGVFFI1865XZZP](/sequence-files/IGVFFI1865XZZP/), [IGVFFI9553XEEI](/sequence-files/IGVFFI9553XEEI/), [IGVFFI8178OKCW](/sequence-files/IGVFFI8178OKCW/), [IGVFFI2898JUNF](/sequence-files/IGVFFI2898JUNF/) 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": "/auxiliary-sets/IGVFDS7027VRZT/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS7733OTCA](/measurement-sets/IGVFDS7733OTCA/) has sequence file(s) [IGVFFI9951YTWY](/sequence-files/IGVFFI9951YTWY/), [IGVFFI4964MYPZ](/sequence-files/IGVFFI4964MYPZ/), [IGVFFI1258BAON](/sequence-files/IGVFFI1258BAON/), [IGVFFI2279LPEK](/sequence-files/IGVFFI2279LPEK/), [IGVFFI1818NNYQ](/sequence-files/IGVFFI1818NNYQ/), [IGVFFI7847OARA](/sequence-files/IGVFFI7847OARA/), [IGVFFI7025NJVQ](/sequence-files/IGVFFI7025NJVQ/), [IGVFFI6643CYLV](/sequence-files/IGVFFI6643CYLV/), [IGVFFI5274KBTZ](/sequence-files/IGVFFI5274KBTZ/), [IGVFFI8663MRYB](/sequence-files/IGVFFI8663MRYB/), [IGVFFI9766DDNU](/sequence-files/IGVFFI9766DDNU/), [IGVFFI4798ZEXE](/sequence-files/IGVFFI4798ZEXE/), [IGVFFI8182EUUN](/sequence-files/IGVFFI8182EUUN/), [IGVFFI3205THSH](/sequence-files/IGVFFI3205THSH/), [IGVFFI9075YCTF](/sequence-files/IGVFFI9075YCTF/), [IGVFFI5373WDMG](/sequence-files/IGVFFI5373WDMG/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS7733OTCA/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7733OTCA](/measurement-sets/IGVFDS7733OTCA/) has sequence file(s): [IGVFFI9951YTWY](/sequence-files/IGVFFI9951YTWY/), [IGVFFI4964MYPZ](/sequence-files/IGVFFI4964MYPZ/), [IGVFFI1258BAON](/sequence-files/IGVFFI1258BAON/), [IGVFFI2279LPEK](/sequence-files/IGVFFI2279LPEK/), [IGVFFI1818NNYQ](/sequence-files/IGVFFI1818NNYQ/), [IGVFFI7847OARA](/sequence-files/IGVFFI7847OARA/), [IGVFFI7025NJVQ](/sequence-files/IGVFFI7025NJVQ/), [IGVFFI6643CYLV](/sequence-files/IGVFFI6643CYLV/), [IGVFFI5274KBTZ](/sequence-files/IGVFFI5274KBTZ/), [IGVFFI8663MRYB](/sequence-files/IGVFFI8663MRYB/), [IGVFFI9766DDNU](/sequence-files/IGVFFI9766DDNU/), [IGVFFI4798ZEXE](/sequence-files/IGVFFI4798ZEXE/), [IGVFFI8182EUUN](/sequence-files/IGVFFI8182EUUN/), [IGVFFI3205THSH](/sequence-files/IGVFFI3205THSH/), [IGVFFI9075YCTF](/sequence-files/IGVFFI9075YCTF/), [IGVFFI5373WDMG](/sequence-files/IGVFFI5373WDMG/) 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/IGVFDS7733OTCA/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS0997MTQA](/auxiliary-sets/IGVFDS0997MTQA/) has sequence file(s) [IGVFFI5758JYDL](/sequence-files/IGVFFI5758JYDL/), [IGVFFI0808FCCO](/sequence-files/IGVFFI0808FCCO/), [IGVFFI7852BFOU](/sequence-files/IGVFFI7852BFOU/), [IGVFFI3938OJKT](/sequence-files/IGVFFI3938OJKT/), [IGVFFI9797JSJB](/sequence-files/IGVFFI9797JSJB/), [IGVFFI2834JYDA](/sequence-files/IGVFFI2834JYDA/), [IGVFFI7620POLB](/sequence-files/IGVFFI7620POLB/), [IGVFFI4290KTZN](/sequence-files/IGVFFI4290KTZN/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS0997MTQA/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS0997MTQA](/auxiliary-sets/IGVFDS0997MTQA/) has sequence file(s): [IGVFFI5758JYDL](/sequence-files/IGVFFI5758JYDL/), [IGVFFI0808FCCO](/sequence-files/IGVFFI0808FCCO/), [IGVFFI7852BFOU](/sequence-files/IGVFFI7852BFOU/), [IGVFFI3938OJKT](/sequence-files/IGVFFI3938OJKT/), [IGVFFI9797JSJB](/sequence-files/IGVFFI9797JSJB/), [IGVFFI2834JYDA](/sequence-files/IGVFFI2834JYDA/), [IGVFFI7620POLB](/sequence-files/IGVFFI7620POLB/), [IGVFFI4290KTZN](/sequence-files/IGVFFI4290KTZN/) 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": "/auxiliary-sets/IGVFDS0997MTQA/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0997MTQA/",
"accession": "IGVFDS0997MTQA",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_sgRNA_LW279"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS7027VRZT/",
"accession": "IGVFDS7027VRZT",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_HTO_LW279"
],
"file_set_type": "cell hashing barcode sequencing",
"status": "preview"
}
],
"award": {
"@id": "/awards/HG011996/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/95d84f03-8ce0-489c-a755-f33ced139c5d/",
"title": "Gary Hon"
},
"title": "Multiscale functional characterization of genomic variation in human developmental disorders"
},
"control_for": [],
"creation_timestamp": "2024-02-21T21:07:19.582954+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1756PPKO/",
"accession": "IGVFDO1756PPKO",
"aliases": [
"igvf:donor_of_WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
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"accession": "IGVFFI9951YTWY",
"aliases": [
"gary-hon:LW279_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:12:49.754251+00:00",
"file_format": "fastq",
"file_size": 64229474,
"href": "/sequence-files/IGVFFI9951YTWY/@@download/IGVFFI9951YTWY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/a5ec765e-0090-427f-a2a3-22410c11bb71/IGVFFI9951YTWY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW279_S17_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4964MYPZ/",
"accession": "IGVFFI4964MYPZ",
"aliases": [
"gary-hon:LW279_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:13:27.697951+00:00",
"file_format": "fastq",
"file_size": 63996232,
"href": "/sequence-files/IGVFFI4964MYPZ/@@download/IGVFFI4964MYPZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/df326d0f-2cd8-43ea-81a9-d6260cd65be1/IGVFFI4964MYPZ.fastq.gz",
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"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "preview",
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"upload_status": "validated"
},
{
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"accession": "IGVFFI1258BAON",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:12:54.182696+00:00",
"file_format": "fastq",
"file_size": 74978563,
"href": "/sequence-files/IGVFFI1258BAON/@@download/IGVFFI1258BAON.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/83e66fd1-1638-4465-918d-1679242b191a/IGVFFI1258BAON.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW279_S17_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2279LPEK/",
"accession": "IGVFFI2279LPEK",
"aliases": [
"gary-hon:LW279_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:12:58.650642+00:00",
"file_format": "fastq",
"file_size": 194288655,
"href": "/sequence-files/IGVFFI2279LPEK/@@download/IGVFFI2279LPEK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/ff1a1ebf-6100-4b39-a44f-6f2c3bc369c5/IGVFFI2279LPEK.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-05-McDermott-NextSeq.10X/2023-10-05/outs/fastq_path/AAC7VLGHV/LW279_S17_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
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"accession": "IGVFFI1818NNYQ",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:13:36.343156+00:00",
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"file_size": 193240864,
"href": "/sequence-files/IGVFFI1818NNYQ/@@download/IGVFFI1818NNYQ.fastq.gz",
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},
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"upload_status": "validated"
},
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"accession": "IGVFFI7847OARA",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:13:04.205621+00:00",
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"href": "/sequence-files/IGVFFI7847OARA/@@download/IGVFFI7847OARA.fastq.gz",
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},
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},
{
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"aliases": [
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],
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"controlled_access": false,
"creation_timestamp": "2024-03-01T17:13:32.053075+00:00",
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},
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},
{
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"accession": "IGVFFI6643CYLV",
"aliases": [
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],
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"controlled_access": false,
"creation_timestamp": "2024-03-01T17:13:41.755030+00:00",
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},
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},
{
"@id": "/sequence-files/IGVFFI5274KBTZ/",
"accession": "IGVFFI5274KBTZ",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T18:50:59.011206+00:00",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8663MRYB/",
"accession": "IGVFFI8663MRYB",
"aliases": [
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],
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"controlled_access": false,
"creation_timestamp": "2024-03-01T18:53:23.636607+00:00",
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},
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},
{
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"aliases": [
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],
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"controlled_access": false,
"creation_timestamp": "2024-03-01T18:50:48.705611+00:00",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4798ZEXE/",
"accession": "IGVFFI4798ZEXE",
"aliases": [
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],
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"controlled_access": false,
"creation_timestamp": "2024-03-01T18:51:36.173094+00:00",
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},
"status": "preview",
"submitted_file_name": "/project/GCRB/Hon_lab/shared/data/sequencing_data/2023/2023-10-02-McDermott-NextSeq.10X/2023-10-02/outs/fastq_path/AAC5W2WHV/LW279_S3_L001_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8182EUUN/",
"accession": "IGVFFI8182EUUN",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T18:51:09.384173+00:00",
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