{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7834BXBN/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7834BXBN",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_LW277"
],
"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 [IGVFDS6231TYIS](/auxiliary-sets/IGVFDS6231TYIS/) has sequence file(s) [IGVFFI3619XUDY](/sequence-files/IGVFFI3619XUDY/), [IGVFFI8623EMUX](/sequence-files/IGVFFI8623EMUX/), [IGVFFI7242OHQZ](/sequence-files/IGVFFI7242OHQZ/), [IGVFFI3194VIYW](/sequence-files/IGVFFI3194VIYW/), [IGVFFI6434GRPO](/sequence-files/IGVFFI6434GRPO/), [IGVFFI5716PBAK](/sequence-files/IGVFFI5716PBAK/), [IGVFFI2229JWQR](/sequence-files/IGVFFI2229JWQR/), [IGVFFI7413XGHD](/sequence-files/IGVFFI7413XGHD/) 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/IGVFDS6231TYIS/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS6231TYIS](/auxiliary-sets/IGVFDS6231TYIS/) has sequence file(s): [IGVFFI3619XUDY](/sequence-files/IGVFFI3619XUDY/), [IGVFFI8623EMUX](/sequence-files/IGVFFI8623EMUX/), [IGVFFI7242OHQZ](/sequence-files/IGVFFI7242OHQZ/), [IGVFFI3194VIYW](/sequence-files/IGVFFI3194VIYW/), [IGVFFI6434GRPO](/sequence-files/IGVFFI6434GRPO/), [IGVFFI5716PBAK](/sequence-files/IGVFFI5716PBAK/), [IGVFFI2229JWQR](/sequence-files/IGVFFI2229JWQR/), [IGVFFI7413XGHD](/sequence-files/IGVFFI7413XGHD/) 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/IGVFDS6231TYIS/"
},
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8280AMDA](/auxiliary-sets/IGVFDS8280AMDA/) has sequence file(s) [IGVFFI6637VQNC](/sequence-files/IGVFFI6637VQNC/), [IGVFFI9225ZAYG](/sequence-files/IGVFFI9225ZAYG/), [IGVFFI7205PTPJ](/sequence-files/IGVFFI7205PTPJ/), [IGVFFI0105QRUB](/sequence-files/IGVFFI0105QRUB/), [IGVFFI5482SCRU](/sequence-files/IGVFFI5482SCRU/), [IGVFFI4436NITM](/sequence-files/IGVFFI4436NITM/), [IGVFFI5870FWJX](/sequence-files/IGVFFI5870FWJX/), [IGVFFI4422CQQU](/sequence-files/IGVFFI4422CQQU/) 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/IGVFDS8280AMDA/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8280AMDA](/auxiliary-sets/IGVFDS8280AMDA/) has sequence file(s): [IGVFFI6637VQNC](/sequence-files/IGVFFI6637VQNC/), [IGVFFI9225ZAYG](/sequence-files/IGVFFI9225ZAYG/), [IGVFFI7205PTPJ](/sequence-files/IGVFFI7205PTPJ/), [IGVFFI0105QRUB](/sequence-files/IGVFFI0105QRUB/), [IGVFFI5482SCRU](/sequence-files/IGVFFI5482SCRU/), [IGVFFI4436NITM](/sequence-files/IGVFFI4436NITM/), [IGVFFI5870FWJX](/sequence-files/IGVFFI5870FWJX/), [IGVFFI4422CQQU](/sequence-files/IGVFFI4422CQQU/) 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/IGVFDS8280AMDA/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS7834BXBN](/measurement-sets/IGVFDS7834BXBN/) has sequence file(s) [IGVFFI2869RZHP](/sequence-files/IGVFFI2869RZHP/), [IGVFFI9035WZGH](/sequence-files/IGVFFI9035WZGH/), [IGVFFI0694FGVK](/sequence-files/IGVFFI0694FGVK/), [IGVFFI4639VVSI](/sequence-files/IGVFFI4639VVSI/), [IGVFFI0927MZKK](/sequence-files/IGVFFI0927MZKK/), [IGVFFI7293GNLQ](/sequence-files/IGVFFI7293GNLQ/), [IGVFFI6030TTPJ](/sequence-files/IGVFFI6030TTPJ/), [IGVFFI3079WTCT](/sequence-files/IGVFFI3079WTCT/), [IGVFFI8109YDPT](/sequence-files/IGVFFI8109YDPT/), [IGVFFI3915NDQI](/sequence-files/IGVFFI3915NDQI/), [IGVFFI7818BGAF](/sequence-files/IGVFFI7818BGAF/), [IGVFFI2196CSLH](/sequence-files/IGVFFI2196CSLH/), [IGVFFI8923KPZG](/sequence-files/IGVFFI8923KPZG/), [IGVFFI1804NWOX](/sequence-files/IGVFFI1804NWOX/), [IGVFFI3609NOVK](/sequence-files/IGVFFI3609NOVK/), [IGVFFI8959OAMJ](/sequence-files/IGVFFI8959OAMJ/) 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/IGVFDS7834BXBN/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7834BXBN](/measurement-sets/IGVFDS7834BXBN/) has sequence file(s): [IGVFFI2869RZHP](/sequence-files/IGVFFI2869RZHP/), [IGVFFI9035WZGH](/sequence-files/IGVFFI9035WZGH/), [IGVFFI0694FGVK](/sequence-files/IGVFFI0694FGVK/), [IGVFFI4639VVSI](/sequence-files/IGVFFI4639VVSI/), [IGVFFI0927MZKK](/sequence-files/IGVFFI0927MZKK/), [IGVFFI7293GNLQ](/sequence-files/IGVFFI7293GNLQ/), [IGVFFI6030TTPJ](/sequence-files/IGVFFI6030TTPJ/), [IGVFFI3079WTCT](/sequence-files/IGVFFI3079WTCT/), [IGVFFI8109YDPT](/sequence-files/IGVFFI8109YDPT/), [IGVFFI3915NDQI](/sequence-files/IGVFFI3915NDQI/), [IGVFFI7818BGAF](/sequence-files/IGVFFI7818BGAF/), [IGVFFI2196CSLH](/sequence-files/IGVFFI2196CSLH/), [IGVFFI8923KPZG](/sequence-files/IGVFFI8923KPZG/), [IGVFFI1804NWOX](/sequence-files/IGVFFI1804NWOX/), [IGVFFI3609NOVK](/sequence-files/IGVFFI3609NOVK/), [IGVFFI8959OAMJ](/sequence-files/IGVFFI8959OAMJ/) 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/IGVFDS7834BXBN/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8280AMDA/",
"accession": "IGVFDS8280AMDA",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_sgRNA_LW277"
],
"file_set_type": "gRNA sequencing",
"status": "preview"
},
{
"@id": "/auxiliary-sets/IGVFDS6231TYIS/",
"accession": "IGVFDS6231TYIS",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_HTO_LW277"
],
"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": "2024-02-21T21:07:17.305831+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": [
{
"@id": "/sequence-files/IGVFFI2869RZHP/",
"accession": "IGVFFI2869RZHP",
"aliases": [
"gary-hon:LW277_1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:07:50.602314+00:00",
"file_format": "fastq",
"file_size": 258302896,
"href": "/sequence-files/IGVFFI2869RZHP/@@download/IGVFFI2869RZHP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/188363b5-a300-4b71-aaea-49d81f1d64f3/IGVFFI2869RZHP.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/LW277_S15_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9035WZGH/",
"accession": "IGVFFI9035WZGH",
"aliases": [
"gary-hon:LW277_1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:07:56.510480+00:00",
"file_format": "fastq",
"file_size": 606482050,
"href": "/sequence-files/IGVFFI9035WZGH/@@download/IGVFFI9035WZGH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/cc888796-2573-4220-8f48-258525a5b1be/IGVFFI9035WZGH.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "preview",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0694FGVK/",
"accession": "IGVFFI0694FGVK",
"aliases": [
"gary-hon:LW277_1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:07:41.475066+00:00",
"file_format": "fastq",
"file_size": 88972214,
"href": "/sequence-files/IGVFFI0694FGVK/@@download/IGVFFI0694FGVK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/0fbd4cc7-f83d-4dd7-8b6c-08bc768b837a/IGVFFI0694FGVK.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/LW277_S15_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4639VVSI/",
"accession": "IGVFFI4639VVSI",
"aliases": [
"gary-hon:LW277_1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:07:46.095112+00:00",
"file_format": "fastq",
"file_size": 91054140,
"href": "/sequence-files/IGVFFI4639VVSI/@@download/IGVFFI4639VVSI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/03/01/c29d3a5f-3e42-4541-97eb-0d08d9aab930/IGVFFI4639VVSI.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/LW277_S15_L001_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0927MZKK/",
"accession": "IGVFFI0927MZKK",
"aliases": [
"gary-hon:LW277_2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:08:05.601004+00:00",
"file_format": "fastq",
"file_size": 88176635,
"href": "/sequence-files/IGVFFI0927MZKK/@@download/IGVFFI0927MZKK.fastq.gz",
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"status": "released",
"term_name": "Illumina NextSeq 2000"
},
"status": "preview",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7293GNLQ/",
"accession": "IGVFFI7293GNLQ",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:08:12.086221+00:00",
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"href": "/sequence-files/IGVFFI7293GNLQ/@@download/IGVFFI7293GNLQ.fastq.gz",
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"status": "released",
"term_name": "Illumina NextSeq 2000"
},
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"upload_status": "validated"
},
{
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"accession": "IGVFFI6030TTPJ",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:08:16.844652+00:00",
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"href": "/sequence-files/IGVFFI6030TTPJ/@@download/IGVFFI6030TTPJ.fastq.gz",
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"status": "released",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3079WTCT/",
"accession": "IGVFFI3079WTCT",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T17:08:22.759644+00:00",
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},
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},
{
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"accession": "IGVFFI8109YDPT",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T18:41:33.530489+00:00",
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},
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"upload_status": "validated"
},
{
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"accession": "IGVFFI3915NDQI",
"aliases": [
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],
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"controlled_access": false,
"creation_timestamp": "2024-03-01T18:41:21.100396+00:00",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7818BGAF/",
"accession": "IGVFFI7818BGAF",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T18:44:04.967011+00:00",
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"status": "released",
"term_name": "Illumina NextSeq 2000"
},
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"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/LW277_S1_L002_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2196CSLH/",
"accession": "IGVFFI2196CSLH",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T18:44:38.968616+00:00",
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"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/2023/2023-10-02-McDermott-NextSeq.10X/2023-10-02/outs/fastq_path/AAC5W2WHV/LW277_S1_L002_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8923KPZG/",
"accession": "IGVFFI8923KPZG",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-03-01T18:41:46.047237+00:00",
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