{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9571BWRT/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9571BWRT",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinC_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 [IGVFSM5553HMSC](/in-vitro-systems/IGVFSM5553HMSC/) has in progress subobject construct library set [IGVFDS2374NXLW](/construct-library-sets/IGVFDS2374NXLW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM5553HMSC/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM5553HMSC](/in-vitro-systems/IGVFSM5553HMSC/) 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/IGVFSM5553HMSC/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS9571BWRT](/measurement-sets/IGVFDS9571BWRT/) 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/IGVFDS9571BWRT/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS9571BWRT](/measurement-sets/IGVFDS9571BWRT/) has sequence file(s) [IGVFFI9163PWKU](/sequence-files/IGVFFI9163PWKU/), [IGVFFI1473RHJI](/sequence-files/IGVFFI1473RHJI/), [IGVFFI2847IJWO](/sequence-files/IGVFFI2847IJWO/), [IGVFFI6362VAKU](/sequence-files/IGVFFI6362VAKU/), [IGVFFI0366RVXY](/sequence-files/IGVFFI0366RVXY/), [IGVFFI3637QTSQ](/sequence-files/IGVFFI3637QTSQ/), [IGVFFI9674YRFE](/sequence-files/IGVFFI9674YRFE/), [IGVFFI2100YJBK](/sequence-files/IGVFFI2100YJBK/), [IGVFFI0806LQXD](/sequence-files/IGVFFI0806LQXD/), [IGVFFI5344GIHZ](/sequence-files/IGVFFI5344GIHZ/), [IGVFFI7771FUKK](/sequence-files/IGVFFI7771FUKK/), [IGVFFI9303YWBP](/sequence-files/IGVFFI9303YWBP/), [IGVFFI9438FFWV](/sequence-files/IGVFFI9438FFWV/), [IGVFFI8646MCTV](/sequence-files/IGVFFI8646MCTV/), [IGVFFI8587DIVE](/sequence-files/IGVFFI8587DIVE/), [IGVFFI9012RFFO](/sequence-files/IGVFFI9012RFFO/), [IGVFFI7942HNDY](/sequence-files/IGVFFI7942HNDY/), [IGVFFI9529AFJP](/sequence-files/IGVFFI9529AFJP/), [IGVFFI3683RKVR](/sequence-files/IGVFFI3683RKVR/), [IGVFFI7837AIQF](/sequence-files/IGVFFI7837AIQF/), [IGVFFI5427BOAK](/sequence-files/IGVFFI5427BOAK/), [IGVFFI8723YIZI](/sequence-files/IGVFFI8723YIZI/), [IGVFFI4897RYLH](/sequence-files/IGVFFI4897RYLH/), [IGVFFI0802AXQK](/sequence-files/IGVFFI0802AXQK/), [IGVFFI8927QBZK](/sequence-files/IGVFFI8927QBZK/), [IGVFFI6932AHRJ](/sequence-files/IGVFFI6932AHRJ/), [IGVFFI7809FCWW](/sequence-files/IGVFFI7809FCWW/), [IGVFFI0860PEYW](/sequence-files/IGVFFI0860PEYW/), [IGVFFI6059CQXT](/sequence-files/IGVFFI6059CQXT/), [IGVFFI6448IQOJ](/sequence-files/IGVFFI6448IQOJ/), [IGVFFI3574NFSF](/sequence-files/IGVFFI3574NFSF/), [IGVFFI6638XTWS](/sequence-files/IGVFFI6638XTWS/), [IGVFFI7918SIPE](/sequence-files/IGVFFI7918SIPE/), [IGVFFI3223ICUH](/sequence-files/IGVFFI3223ICUH/), [IGVFFI7085FRRK](/sequence-files/IGVFFI7085FRRK/), [IGVFFI9094FEXS](/sequence-files/IGVFFI9094FEXS/), [IGVFFI0549SHDW](/sequence-files/IGVFFI0549SHDW/), [IGVFFI1565IYIK](/sequence-files/IGVFFI1565IYIK/), [IGVFFI1697QMTO](/sequence-files/IGVFFI1697QMTO/), [IGVFFI5774NHHM](/sequence-files/IGVFFI5774NHHM/), [IGVFFI8100NFAY](/sequence-files/IGVFFI8100NFAY/), [IGVFFI7712IPYT](/sequence-files/IGVFFI7712IPYT/), [IGVFFI6271FAOS](/sequence-files/IGVFFI6271FAOS/), [IGVFFI0778JHDP](/sequence-files/IGVFFI0778JHDP/), [IGVFFI9103QGHK](/sequence-files/IGVFFI9103QGHK/), [IGVFFI3064COLS](/sequence-files/IGVFFI3064COLS/), [IGVFFI1831CQZA](/sequence-files/IGVFFI1831CQZA/), [IGVFFI3292EQHB](/sequence-files/IGVFFI3292EQHB/) 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/IGVFDS9571BWRT/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9571BWRT](/measurement-sets/IGVFDS9571BWRT/) has sequence file(s): [IGVFFI9163PWKU](/sequence-files/IGVFFI9163PWKU/), [IGVFFI1473RHJI](/sequence-files/IGVFFI1473RHJI/), [IGVFFI2847IJWO](/sequence-files/IGVFFI2847IJWO/), [IGVFFI6362VAKU](/sequence-files/IGVFFI6362VAKU/), [IGVFFI0366RVXY](/sequence-files/IGVFFI0366RVXY/), [IGVFFI3637QTSQ](/sequence-files/IGVFFI3637QTSQ/), [IGVFFI9674YRFE](/sequence-files/IGVFFI9674YRFE/), [IGVFFI2100YJBK](/sequence-files/IGVFFI2100YJBK/), [IGVFFI0806LQXD](/sequence-files/IGVFFI0806LQXD/), [IGVFFI5344GIHZ](/sequence-files/IGVFFI5344GIHZ/), [IGVFFI7771FUKK](/sequence-files/IGVFFI7771FUKK/), [IGVFFI9303YWBP](/sequence-files/IGVFFI9303YWBP/), [IGVFFI9438FFWV](/sequence-files/IGVFFI9438FFWV/), [IGVFFI8646MCTV](/sequence-files/IGVFFI8646MCTV/), [IGVFFI8587DIVE](/sequence-files/IGVFFI8587DIVE/), [IGVFFI9012RFFO](/sequence-files/IGVFFI9012RFFO/), [IGVFFI7942HNDY](/sequence-files/IGVFFI7942HNDY/), [IGVFFI9529AFJP](/sequence-files/IGVFFI9529AFJP/), [IGVFFI3683RKVR](/sequence-files/IGVFFI3683RKVR/), [IGVFFI7837AIQF](/sequence-files/IGVFFI7837AIQF/), [IGVFFI5427BOAK](/sequence-files/IGVFFI5427BOAK/), [IGVFFI8723YIZI](/sequence-files/IGVFFI8723YIZI/), [IGVFFI4897RYLH](/sequence-files/IGVFFI4897RYLH/), [IGVFFI0802AXQK](/sequence-files/IGVFFI0802AXQK/), [IGVFFI8927QBZK](/sequence-files/IGVFFI8927QBZK/), [IGVFFI6932AHRJ](/sequence-files/IGVFFI6932AHRJ/), [IGVFFI7809FCWW](/sequence-files/IGVFFI7809FCWW/), [IGVFFI0860PEYW](/sequence-files/IGVFFI0860PEYW/), [IGVFFI6059CQXT](/sequence-files/IGVFFI6059CQXT/), [IGVFFI6448IQOJ](/sequence-files/IGVFFI6448IQOJ/), [IGVFFI3574NFSF](/sequence-files/IGVFFI3574NFSF/), [IGVFFI6638XTWS](/sequence-files/IGVFFI6638XTWS/), [IGVFFI7918SIPE](/sequence-files/IGVFFI7918SIPE/), [IGVFFI3223ICUH](/sequence-files/IGVFFI3223ICUH/), [IGVFFI7085FRRK](/sequence-files/IGVFFI7085FRRK/), [IGVFFI9094FEXS](/sequence-files/IGVFFI9094FEXS/), [IGVFFI0549SHDW](/sequence-files/IGVFFI0549SHDW/), [IGVFFI1565IYIK](/sequence-files/IGVFFI1565IYIK/), [IGVFFI1697QMTO](/sequence-files/IGVFFI1697QMTO/), [IGVFFI5774NHHM](/sequence-files/IGVFFI5774NHHM/), [IGVFFI8100NFAY](/sequence-files/IGVFFI8100NFAY/), [IGVFFI7712IPYT](/sequence-files/IGVFFI7712IPYT/), [IGVFFI6271FAOS](/sequence-files/IGVFFI6271FAOS/), [IGVFFI0778JHDP](/sequence-files/IGVFFI0778JHDP/), [IGVFFI9103QGHK](/sequence-files/IGVFFI9103QGHK/), [IGVFFI3064COLS](/sequence-files/IGVFFI3064COLS/), [IGVFFI1831CQZA](/sequence-files/IGVFFI1831CQZA/), [IGVFFI3292EQHB](/sequence-files/IGVFFI3292EQHB/) 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/IGVFDS9571BWRT/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS9571BWRT](/measurement-sets/IGVFDS9571BWRT/) 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/IGVFDS9571BWRT/"
}
]
},
"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/IGVFDS2374NXLW/",
"accession": "IGVFDS2374NXLW",
"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/IGVFDS4989HPTW/",
"accession": "IGVFDS4989HPTW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"creation_timestamp": "2023-12-01T00:04:44.582533+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"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": [
{
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"accession": "IGVFFI9163PWKU",
"aliases": [
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],
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"controlled_access": false,
"creation_timestamp": "2023-12-05T19:32:57.011313+00:00",
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"md5sum": "d70cad7d382e6cf630606b057d39c918",
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"sequencing_platform": {
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"term_name": "Illumina NextSeq 550"
},
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"upload_status": "validated"
},
{
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],
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},
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},
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},
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},
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},
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},
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},
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},
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},
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},
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},
{
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],
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"s3_uri": "s3://igvf-files/2023/12/05/e7702325-986d-481a-beef-2bee5fd307a0/IGVFFI1831CQZA.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinC-PCRrep11_S125_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3292EQHB/",
"accession": "IGVFFI3292EQHB",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinC-PCRrep10_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:26:45.511420+00:00",
"file_format": "fastq",
"file_size": 6923246,
"href": "/sequence-files/IGVFFI3292EQHB/@@download/IGVFFI3292EQHB.fastq.gz",
"md5sum": "eb980d7dada06f9afd7397b7a6e69f33",
"s3_uri": "s3://igvf-files/2023/12/05/f28fe939-f26f-4772-924d-82a7e122d628/IGVFFI3292EQHB.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinC-PCRrep10_S124_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5031MNRR/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set. This measurement set previously used Variant FlowFISH as a preferred_assay_title, but this enum is now removed. So it has been defaulted to Variant-EFFECTS.",
"preferred_assay_title": "Variant-EFFECTS",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"release_timestamp": "2023-12-20T23:06:57.510049+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5553HMSC/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5553HMSC",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep1-BinC"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:THP-1"
],
"status": "released",
"summary": "THP-1",
"term_name": "THP-1"
}
],
"status": "released",
"summary": "Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 51-75% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
}
],
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"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T19:25:40.244528+00:00",
"summary": "CRISPR prime editing Variant-EFFECTS sorted on the expression of PPIF integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"targeted_genes": [
{
"@id": "/genes/ENSG00000108179/",
"geneid": "ENSG00000108179",
"name": "peptidylprolyl isomerase F",
"status": "released",
"symbol": "PPIF",
"synonyms": [
"PPIase F",
"peptidylprolyl isomerase F",
"Cyp-D",
"peptidyl-prolyl cis-trans isomerase F, mitochondrial",
"PPIF",
"CyP-M",
"cyclophilin F",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"cyclophilin 3",
"cyclophilin D",
"rotamase F",
"mitochondrial cyclophilin",
"CypD",
"CYP3"
]
}
],
"uuid": "0bc8eb39-dac6-4c4c-82d5-348f89325d97"
}