{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2059ELNJ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2059ELNJ",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-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 [IGVFSM2837HWZC](/in-vitro-systems/IGVFSM2837HWZC/) 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/IGVFSM2837HWZC/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM2837HWZC](/in-vitro-systems/IGVFSM2837HWZC/) 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/IGVFSM2837HWZC/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS2059ELNJ](/measurement-sets/IGVFDS2059ELNJ/) 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/IGVFDS2059ELNJ/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2059ELNJ](/measurement-sets/IGVFDS2059ELNJ/) has sequence file(s) [IGVFFI9684DAXI](/sequence-files/IGVFFI9684DAXI/), [IGVFFI5053EKGY](/sequence-files/IGVFFI5053EKGY/), [IGVFFI0097TTTU](/sequence-files/IGVFFI0097TTTU/), [IGVFFI0846ZEJX](/sequence-files/IGVFFI0846ZEJX/), [IGVFFI1811JPVS](/sequence-files/IGVFFI1811JPVS/), [IGVFFI1289PZQN](/sequence-files/IGVFFI1289PZQN/), [IGVFFI9507ROFB](/sequence-files/IGVFFI9507ROFB/), [IGVFFI0892STFJ](/sequence-files/IGVFFI0892STFJ/), [IGVFFI8940VKWU](/sequence-files/IGVFFI8940VKWU/), [IGVFFI6555CXIT](/sequence-files/IGVFFI6555CXIT/), [IGVFFI0026LASN](/sequence-files/IGVFFI0026LASN/), [IGVFFI1196VCMU](/sequence-files/IGVFFI1196VCMU/), [IGVFFI8968FVOI](/sequence-files/IGVFFI8968FVOI/), [IGVFFI9821CKCH](/sequence-files/IGVFFI9821CKCH/), [IGVFFI2235HZQI](/sequence-files/IGVFFI2235HZQI/), [IGVFFI5534MNRR](/sequence-files/IGVFFI5534MNRR/), [IGVFFI2593RLFA](/sequence-files/IGVFFI2593RLFA/), [IGVFFI6539JGYH](/sequence-files/IGVFFI6539JGYH/), [IGVFFI0915HDSO](/sequence-files/IGVFFI0915HDSO/), [IGVFFI9905YAKB](/sequence-files/IGVFFI9905YAKB/), [IGVFFI8252SIEN](/sequence-files/IGVFFI8252SIEN/), [IGVFFI4894TZCD](/sequence-files/IGVFFI4894TZCD/), [IGVFFI8632KYNX](/sequence-files/IGVFFI8632KYNX/), [IGVFFI7361UJGY](/sequence-files/IGVFFI7361UJGY/), [IGVFFI3356QHCN](/sequence-files/IGVFFI3356QHCN/), [IGVFFI2690ISTB](/sequence-files/IGVFFI2690ISTB/), [IGVFFI9449WBJF](/sequence-files/IGVFFI9449WBJF/), [IGVFFI7487YGRQ](/sequence-files/IGVFFI7487YGRQ/), [IGVFFI6307IRFG](/sequence-files/IGVFFI6307IRFG/), [IGVFFI7249UYXY](/sequence-files/IGVFFI7249UYXY/), [IGVFFI6460DGXS](/sequence-files/IGVFFI6460DGXS/), [IGVFFI3881VVDO](/sequence-files/IGVFFI3881VVDO/), [IGVFFI6048UGXE](/sequence-files/IGVFFI6048UGXE/), [IGVFFI3914HYDK](/sequence-files/IGVFFI3914HYDK/), [IGVFFI5009OVAI](/sequence-files/IGVFFI5009OVAI/), [IGVFFI0188UUQW](/sequence-files/IGVFFI0188UUQW/), [IGVFFI7695QFZR](/sequence-files/IGVFFI7695QFZR/), [IGVFFI5592UBKN](/sequence-files/IGVFFI5592UBKN/), [IGVFFI4891OGFV](/sequence-files/IGVFFI4891OGFV/), [IGVFFI3297NDOC](/sequence-files/IGVFFI3297NDOC/), [IGVFFI2493BVGX](/sequence-files/IGVFFI2493BVGX/), [IGVFFI7836HQUM](/sequence-files/IGVFFI7836HQUM/), [IGVFFI1345FKXM](/sequence-files/IGVFFI1345FKXM/), [IGVFFI7614JCYR](/sequence-files/IGVFFI7614JCYR/), [IGVFFI3273LJUE](/sequence-files/IGVFFI3273LJUE/), [IGVFFI4330ICMC](/sequence-files/IGVFFI4330ICMC/), [IGVFFI8327XBXF](/sequence-files/IGVFFI8327XBXF/), [IGVFFI5263TVYB](/sequence-files/IGVFFI5263TVYB/) 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/IGVFDS2059ELNJ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2059ELNJ](/measurement-sets/IGVFDS2059ELNJ/) has sequence file(s): [IGVFFI9684DAXI](/sequence-files/IGVFFI9684DAXI/), [IGVFFI5053EKGY](/sequence-files/IGVFFI5053EKGY/), [IGVFFI0097TTTU](/sequence-files/IGVFFI0097TTTU/), [IGVFFI0846ZEJX](/sequence-files/IGVFFI0846ZEJX/), [IGVFFI1811JPVS](/sequence-files/IGVFFI1811JPVS/), [IGVFFI1289PZQN](/sequence-files/IGVFFI1289PZQN/), [IGVFFI9507ROFB](/sequence-files/IGVFFI9507ROFB/), [IGVFFI0892STFJ](/sequence-files/IGVFFI0892STFJ/), [IGVFFI8940VKWU](/sequence-files/IGVFFI8940VKWU/), [IGVFFI6555CXIT](/sequence-files/IGVFFI6555CXIT/), [IGVFFI0026LASN](/sequence-files/IGVFFI0026LASN/), [IGVFFI1196VCMU](/sequence-files/IGVFFI1196VCMU/), [IGVFFI8968FVOI](/sequence-files/IGVFFI8968FVOI/), [IGVFFI9821CKCH](/sequence-files/IGVFFI9821CKCH/), [IGVFFI2235HZQI](/sequence-files/IGVFFI2235HZQI/), [IGVFFI5534MNRR](/sequence-files/IGVFFI5534MNRR/), [IGVFFI2593RLFA](/sequence-files/IGVFFI2593RLFA/), [IGVFFI6539JGYH](/sequence-files/IGVFFI6539JGYH/), [IGVFFI0915HDSO](/sequence-files/IGVFFI0915HDSO/), [IGVFFI9905YAKB](/sequence-files/IGVFFI9905YAKB/), [IGVFFI8252SIEN](/sequence-files/IGVFFI8252SIEN/), [IGVFFI4894TZCD](/sequence-files/IGVFFI4894TZCD/), [IGVFFI8632KYNX](/sequence-files/IGVFFI8632KYNX/), [IGVFFI7361UJGY](/sequence-files/IGVFFI7361UJGY/), [IGVFFI3356QHCN](/sequence-files/IGVFFI3356QHCN/), [IGVFFI2690ISTB](/sequence-files/IGVFFI2690ISTB/), [IGVFFI9449WBJF](/sequence-files/IGVFFI9449WBJF/), [IGVFFI7487YGRQ](/sequence-files/IGVFFI7487YGRQ/), [IGVFFI6307IRFG](/sequence-files/IGVFFI6307IRFG/), [IGVFFI7249UYXY](/sequence-files/IGVFFI7249UYXY/), [IGVFFI6460DGXS](/sequence-files/IGVFFI6460DGXS/), [IGVFFI3881VVDO](/sequence-files/IGVFFI3881VVDO/), [IGVFFI6048UGXE](/sequence-files/IGVFFI6048UGXE/), [IGVFFI3914HYDK](/sequence-files/IGVFFI3914HYDK/), [IGVFFI5009OVAI](/sequence-files/IGVFFI5009OVAI/), [IGVFFI0188UUQW](/sequence-files/IGVFFI0188UUQW/), [IGVFFI7695QFZR](/sequence-files/IGVFFI7695QFZR/), [IGVFFI5592UBKN](/sequence-files/IGVFFI5592UBKN/), [IGVFFI4891OGFV](/sequence-files/IGVFFI4891OGFV/), [IGVFFI3297NDOC](/sequence-files/IGVFFI3297NDOC/), [IGVFFI2493BVGX](/sequence-files/IGVFFI2493BVGX/), [IGVFFI7836HQUM](/sequence-files/IGVFFI7836HQUM/), [IGVFFI1345FKXM](/sequence-files/IGVFFI1345FKXM/), [IGVFFI7614JCYR](/sequence-files/IGVFFI7614JCYR/), [IGVFFI3273LJUE](/sequence-files/IGVFFI3273LJUE/), [IGVFFI4330ICMC](/sequence-files/IGVFFI4330ICMC/), [IGVFFI8327XBXF](/sequence-files/IGVFFI8327XBXF/), [IGVFFI5263TVYB](/sequence-files/IGVFFI5263TVYB/) 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/IGVFDS2059ELNJ/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2059ELNJ](/measurement-sets/IGVFDS2059ELNJ/) 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/IGVFDS2059ELNJ/"
}
]
},
"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": "2023-11-30T22:48:54.840589+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": "IGVFFI9684DAXI",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinB-PCRrep12_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:53:42.772807+00:00",
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"file_size": 1340507,
"href": "/sequence-files/IGVFFI9684DAXI/@@download/IGVFFI9684DAXI.fastq.gz",
"md5sum": "3383062ae84c3343410f8decf053a1f6",
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"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-FFrep2-BinB-PCRrep12_S162_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5053EKGY/",
"accession": "IGVFFI5053EKGY",
"aliases": [
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],
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"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0097TTTU/",
"accession": "IGVFFI0097TTTU",
"aliases": [
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],
"content_type": "reads",
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},
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},
{
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},
{
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"aliases": [
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],
"content_type": "reads",
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},
"status": "released",
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},
{
"@id": "/sequence-files/IGVFFI1289PZQN/",
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],
"content_type": "reads",
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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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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8940VKWU/",
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"aliases": [
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],
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6555CXIT/",
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"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:57:16.779281+00:00",
"file_format": "fastq",
"file_size": 1571301,
"href": "/sequence-files/IGVFFI8327XBXF/@@download/IGVFFI8327XBXF.fastq.gz",
"md5sum": "cbef3d742bb2951a4b0c827a2289a68e",
"s3_uri": "s3://igvf-files/2023/12/05/faee6664-0b52-4cab-a52f-96f1b1a9bf69/IGVFFI8327XBXF.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinB-PCRrep7_S157_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5263TVYB/",
"accession": "IGVFFI5263TVYB",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinB-PCRrep6_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:56:57.991335+00:00",
"file_format": "fastq",
"file_size": 3555789,
"href": "/sequence-files/IGVFFI5263TVYB/@@download/IGVFFI5263TVYB.fastq.gz",
"md5sum": "32ee7b7203868c7f89bc29b98a84060e",
"s3_uri": "s3://igvf-files/2023/12/05/2e63a6f2-fd94-434c-b0d7-83d728e1c41b/IGVFFI5263TVYB.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-FFrep2-BinB-PCRrep6_S66_R1_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": "2023-12-20T23:07:06.274740+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2837HWZC/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2837HWZC",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep2-BinB"
],
"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 26-50% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T19:51:43.243092+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": "dc6751d9-4e61-4b41-962b-0b8c34a84adc"
}