{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1674OUCP/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1674OUCP",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinB_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"assay_slims": [
"CRISPR screens"
],
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM5175SJIS](/in-vitro-systems/IGVFSM5175SJIS/) has in progress subobject construct library set [IGVFDS6982DESN](/construct-library-sets/IGVFDS6982DESN/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM5175SJIS/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM5175SJIS](/in-vitro-systems/IGVFSM5175SJIS/) 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": "/in-vitro-systems/IGVFSM5175SJIS/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS1674OUCP](/measurement-sets/IGVFDS1674OUCP/) 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/IGVFDS1674OUCP/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS1674OUCP](/measurement-sets/IGVFDS1674OUCP/) has sequence file(s) [IGVFFI7962GJRR](/sequence-files/IGVFFI7962GJRR/), [IGVFFI9542KCAO](/sequence-files/IGVFFI9542KCAO/), [IGVFFI0214WBSJ](/sequence-files/IGVFFI0214WBSJ/), [IGVFFI0743HDYX](/sequence-files/IGVFFI0743HDYX/), [IGVFFI5400UUAG](/sequence-files/IGVFFI5400UUAG/), [IGVFFI5678VPXX](/sequence-files/IGVFFI5678VPXX/), [IGVFFI7258EDPE](/sequence-files/IGVFFI7258EDPE/), [IGVFFI1386LWQL](/sequence-files/IGVFFI1386LWQL/), [IGVFFI5351OTLF](/sequence-files/IGVFFI5351OTLF/), [IGVFFI7517LZRN](/sequence-files/IGVFFI7517LZRN/), [IGVFFI1130BHXT](/sequence-files/IGVFFI1130BHXT/), [IGVFFI4322GXDN](/sequence-files/IGVFFI4322GXDN/), [IGVFFI6351WIQM](/sequence-files/IGVFFI6351WIQM/), [IGVFFI6266UDFP](/sequence-files/IGVFFI6266UDFP/), [IGVFFI6421DUIN](/sequence-files/IGVFFI6421DUIN/), [IGVFFI0838ASIK](/sequence-files/IGVFFI0838ASIK/), [IGVFFI8537GUKD](/sequence-files/IGVFFI8537GUKD/), [IGVFFI1284VLMR](/sequence-files/IGVFFI1284VLMR/), [IGVFFI5261FRGH](/sequence-files/IGVFFI5261FRGH/), [IGVFFI9938QWWM](/sequence-files/IGVFFI9938QWWM/), [IGVFFI2164BSLS](/sequence-files/IGVFFI2164BSLS/), [IGVFFI9792LJET](/sequence-files/IGVFFI9792LJET/), [IGVFFI0849TYIU](/sequence-files/IGVFFI0849TYIU/), [IGVFFI6449QZQS](/sequence-files/IGVFFI6449QZQS/), [IGVFFI1324VPBT](/sequence-files/IGVFFI1324VPBT/), [IGVFFI7722NGHW](/sequence-files/IGVFFI7722NGHW/), [IGVFFI6849EKQE](/sequence-files/IGVFFI6849EKQE/), [IGVFFI8900KHJR](/sequence-files/IGVFFI8900KHJR/), [IGVFFI6064CFCZ](/sequence-files/IGVFFI6064CFCZ/), [IGVFFI2751SFWM](/sequence-files/IGVFFI2751SFWM/), [IGVFFI8382VXTU](/sequence-files/IGVFFI8382VXTU/), [IGVFFI9794IIIZ](/sequence-files/IGVFFI9794IIIZ/), [IGVFFI3995QWEQ](/sequence-files/IGVFFI3995QWEQ/), [IGVFFI4353ADRG](/sequence-files/IGVFFI4353ADRG/), [IGVFFI8765BEHK](/sequence-files/IGVFFI8765BEHK/), [IGVFFI9043GWJF](/sequence-files/IGVFFI9043GWJF/), [IGVFFI9019KSGN](/sequence-files/IGVFFI9019KSGN/), [IGVFFI7224DCNP](/sequence-files/IGVFFI7224DCNP/), [IGVFFI6394HZYT](/sequence-files/IGVFFI6394HZYT/), [IGVFFI8886MCBY](/sequence-files/IGVFFI8886MCBY/), [IGVFFI4121DCCA](/sequence-files/IGVFFI4121DCCA/), [IGVFFI4091QUCN](/sequence-files/IGVFFI4091QUCN/), [IGVFFI8736TVDQ](/sequence-files/IGVFFI8736TVDQ/), [IGVFFI9371CZGA](/sequence-files/IGVFFI9371CZGA/), [IGVFFI9021CNLQ](/sequence-files/IGVFFI9021CNLQ/), [IGVFFI3363HDKQ](/sequence-files/IGVFFI3363HDKQ/), [IGVFFI8666HUSZ](/sequence-files/IGVFFI8666HUSZ/), [IGVFFI4325RPSE](/sequence-files/IGVFFI4325RPSE/) which lack specification of a `sequencing_kit`. Sequence files in a file set associated wtih bulk data should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS1674OUCP/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1674OUCP](/measurement-sets/IGVFDS1674OUCP/) has sequence file(s): [IGVFFI7962GJRR](/sequence-files/IGVFFI7962GJRR/), [IGVFFI9542KCAO](/sequence-files/IGVFFI9542KCAO/), [IGVFFI0214WBSJ](/sequence-files/IGVFFI0214WBSJ/), [IGVFFI0743HDYX](/sequence-files/IGVFFI0743HDYX/), [IGVFFI5400UUAG](/sequence-files/IGVFFI5400UUAG/), [IGVFFI5678VPXX](/sequence-files/IGVFFI5678VPXX/), [IGVFFI7258EDPE](/sequence-files/IGVFFI7258EDPE/), [IGVFFI1386LWQL](/sequence-files/IGVFFI1386LWQL/), [IGVFFI5351OTLF](/sequence-files/IGVFFI5351OTLF/), [IGVFFI7517LZRN](/sequence-files/IGVFFI7517LZRN/), [IGVFFI1130BHXT](/sequence-files/IGVFFI1130BHXT/), [IGVFFI4322GXDN](/sequence-files/IGVFFI4322GXDN/), [IGVFFI6351WIQM](/sequence-files/IGVFFI6351WIQM/), [IGVFFI6266UDFP](/sequence-files/IGVFFI6266UDFP/), [IGVFFI6421DUIN](/sequence-files/IGVFFI6421DUIN/), [IGVFFI0838ASIK](/sequence-files/IGVFFI0838ASIK/), [IGVFFI8537GUKD](/sequence-files/IGVFFI8537GUKD/), [IGVFFI1284VLMR](/sequence-files/IGVFFI1284VLMR/), [IGVFFI5261FRGH](/sequence-files/IGVFFI5261FRGH/), [IGVFFI9938QWWM](/sequence-files/IGVFFI9938QWWM/), [IGVFFI2164BSLS](/sequence-files/IGVFFI2164BSLS/), [IGVFFI9792LJET](/sequence-files/IGVFFI9792LJET/), [IGVFFI0849TYIU](/sequence-files/IGVFFI0849TYIU/), [IGVFFI6449QZQS](/sequence-files/IGVFFI6449QZQS/), [IGVFFI1324VPBT](/sequence-files/IGVFFI1324VPBT/), [IGVFFI7722NGHW](/sequence-files/IGVFFI7722NGHW/), [IGVFFI6849EKQE](/sequence-files/IGVFFI6849EKQE/), [IGVFFI8900KHJR](/sequence-files/IGVFFI8900KHJR/), [IGVFFI6064CFCZ](/sequence-files/IGVFFI6064CFCZ/), [IGVFFI2751SFWM](/sequence-files/IGVFFI2751SFWM/), [IGVFFI8382VXTU](/sequence-files/IGVFFI8382VXTU/), [IGVFFI9794IIIZ](/sequence-files/IGVFFI9794IIIZ/), [IGVFFI3995QWEQ](/sequence-files/IGVFFI3995QWEQ/), [IGVFFI4353ADRG](/sequence-files/IGVFFI4353ADRG/), [IGVFFI8765BEHK](/sequence-files/IGVFFI8765BEHK/), [IGVFFI9043GWJF](/sequence-files/IGVFFI9043GWJF/), [IGVFFI9019KSGN](/sequence-files/IGVFFI9019KSGN/), [IGVFFI7224DCNP](/sequence-files/IGVFFI7224DCNP/), [IGVFFI6394HZYT](/sequence-files/IGVFFI6394HZYT/), [IGVFFI8886MCBY](/sequence-files/IGVFFI8886MCBY/), [IGVFFI4121DCCA](/sequence-files/IGVFFI4121DCCA/), [IGVFFI4091QUCN](/sequence-files/IGVFFI4091QUCN/), [IGVFFI8736TVDQ](/sequence-files/IGVFFI8736TVDQ/), [IGVFFI9371CZGA](/sequence-files/IGVFFI9371CZGA/), [IGVFFI9021CNLQ](/sequence-files/IGVFFI9021CNLQ/), [IGVFFI3363HDKQ](/sequence-files/IGVFFI3363HDKQ/), [IGVFFI8666HUSZ](/sequence-files/IGVFFI8666HUSZ/), [IGVFFI4325RPSE](/sequence-files/IGVFFI4325RPSE/) which do not have any `seqspecs`. Sequence files in a file set associated with bulk data are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS1674OUCP/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1674OUCP](/measurement-sets/IGVFDS1674OUCP/) has no cell sorting `auxiliary_sets`. CRISPR-based measurement sets that utilize flow cytometry are expected to link to a cell sorting auxiliary set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS1674OUCP/"
}
]
},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6982DESN/",
"accession": "IGVFDS6982DESN",
"file_set_type": "guide library",
"status": "in progress",
"summary": "guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"control_file_sets": [
{
"@id": "/measurement-sets/IGVFDS5864UGFT/",
"accession": "IGVFDS5864UGFT",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:49:58.994962+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI7962GJRR/",
"accession": "IGVFFI7962GJRR",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep3_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:11:42.864534+00:00",
"file_format": "fastq",
"file_size": 1583714,
"href": "/sequence-files/IGVFFI7962GJRR/@@download/IGVFFI7962GJRR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/4daf2a2f-4cfc-4fe1-9833-a8bc30069363/IGVFFI7962GJRR.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep3_S255_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9542KCAO/",
"accession": "IGVFFI9542KCAO",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep11_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:10:24.167286+00:00",
"file_format": "fastq",
"file_size": 5491691,
"href": "/sequence-files/IGVFFI9542KCAO/@@download/IGVFFI9542KCAO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/7c0495e9-cc46-4529-842f-cd5f0730dc16/IGVFFI9542KCAO.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep11_S263_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0214WBSJ/",
"accession": "IGVFFI0214WBSJ",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:11:07.915912+00:00",
"file_format": "fastq",
"file_size": 1319448,
"href": "/sequence-files/IGVFFI0214WBSJ/@@download/IGVFFI0214WBSJ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/808fbe3b-6bb0-4669-b5be-e8e55a898f4f/IGVFFI0214WBSJ.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep2_S254_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0743HDYX/",
"accession": "IGVFFI0743HDYX",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep3_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:11:51.529612+00:00",
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"file_size": 1342463,
"href": "/sequence-files/IGVFFI0743HDYX/@@download/IGVFFI0743HDYX.fastq.gz",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5400UUAG/",
"accession": "IGVFFI5400UUAG",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:08:53.169120+00:00",
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"href": "/sequence-files/IGVFFI5400UUAG/@@download/IGVFFI5400UUAG.fastq.gz",
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"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
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"accession": "IGVFFI5678VPXX",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:13:27.885956+00:00",
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"file_size": 1517416,
"href": "/sequence-files/IGVFFI5678VPXX/@@download/IGVFFI5678VPXX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/7afe9105-2d25-4c5c-a0eb-e0aecf5eea42/IGVFFI5678VPXX.fastq.gz",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep6_S258_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7258EDPE/",
"accession": "IGVFFI7258EDPE",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:12:44.343122+00:00",
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"href": "/sequence-files/IGVFFI7258EDPE/@@download/IGVFFI7258EDPE.fastq.gz",
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},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1386LWQL/",
"accession": "IGVFFI1386LWQL",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:13:54.064202+00:00",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5351OTLF/",
"accession": "IGVFFI5351OTLF",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:09:10.644715+00:00",
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"href": "/sequence-files/IGVFFI5351OTLF/@@download/IGVFFI5351OTLF.fastq.gz",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep1_S253_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7517LZRN/",
"accession": "IGVFFI7517LZRN",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:10:50.130775+00:00",
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"file_size": 4040224,
"href": "/sequence-files/IGVFFI7517LZRN/@@download/IGVFFI7517LZRN.fastq.gz",
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinB-PCRrep12_S264_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1130BHXT/",
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"CyP-M",
"cyclophilin F",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"cyclophilin 3",
"cyclophilin D",
"rotamase F",
"mitochondrial cyclophilin",
"CypD",
"CYP3"
]
}
],
"uuid": "c77529f8-ec2c-48e2-ae55-87aad932b827"
}