{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4761PXVO/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4761PXVO",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinA_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": "missing publication",
"detail": "Measurement set [IGVFDS4761PXVO](/measurement-sets/IGVFDS4761PXVO/) 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/IGVFDS4761PXVO/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS4761PXVO](/measurement-sets/IGVFDS4761PXVO/) has sequence file(s) [IGVFFI1227JYHU](/sequence-files/IGVFFI1227JYHU/), [IGVFFI0602HGYD](/sequence-files/IGVFFI0602HGYD/), [IGVFFI3716GUMG](/sequence-files/IGVFFI3716GUMG/), [IGVFFI3034OZUL](/sequence-files/IGVFFI3034OZUL/), [IGVFFI7325CDOX](/sequence-files/IGVFFI7325CDOX/), [IGVFFI2191QBIE](/sequence-files/IGVFFI2191QBIE/), [IGVFFI8321VUAU](/sequence-files/IGVFFI8321VUAU/), [IGVFFI4288XHUX](/sequence-files/IGVFFI4288XHUX/), [IGVFFI3808JEKJ](/sequence-files/IGVFFI3808JEKJ/), [IGVFFI7789LABZ](/sequence-files/IGVFFI7789LABZ/), [IGVFFI3933SRWS](/sequence-files/IGVFFI3933SRWS/), [IGVFFI1576FWBE](/sequence-files/IGVFFI1576FWBE/), [IGVFFI6197DOEG](/sequence-files/IGVFFI6197DOEG/), [IGVFFI4927AFPV](/sequence-files/IGVFFI4927AFPV/), [IGVFFI9943RVHV](/sequence-files/IGVFFI9943RVHV/), [IGVFFI6602JMCV](/sequence-files/IGVFFI6602JMCV/), [IGVFFI0030DFFN](/sequence-files/IGVFFI0030DFFN/), [IGVFFI9423LSSX](/sequence-files/IGVFFI9423LSSX/), [IGVFFI1189WLQL](/sequence-files/IGVFFI1189WLQL/), [IGVFFI7066PBGZ](/sequence-files/IGVFFI7066PBGZ/), [IGVFFI5556XSRH](/sequence-files/IGVFFI5556XSRH/), [IGVFFI6629JRKX](/sequence-files/IGVFFI6629JRKX/), [IGVFFI1631MQVE](/sequence-files/IGVFFI1631MQVE/), [IGVFFI5479QUYU](/sequence-files/IGVFFI5479QUYU/), [IGVFFI5561PSUU](/sequence-files/IGVFFI5561PSUU/), [IGVFFI8119ONEN](/sequence-files/IGVFFI8119ONEN/), [IGVFFI7985BQOY](/sequence-files/IGVFFI7985BQOY/), [IGVFFI7638KMFR](/sequence-files/IGVFFI7638KMFR/), [IGVFFI1570DCMH](/sequence-files/IGVFFI1570DCMH/), [IGVFFI5947BHMQ](/sequence-files/IGVFFI5947BHMQ/), [IGVFFI3204GLEE](/sequence-files/IGVFFI3204GLEE/), [IGVFFI3036CLFS](/sequence-files/IGVFFI3036CLFS/), [IGVFFI9131RVAG](/sequence-files/IGVFFI9131RVAG/), [IGVFFI1753ZLCW](/sequence-files/IGVFFI1753ZLCW/), [IGVFFI9671KRGE](/sequence-files/IGVFFI9671KRGE/), [IGVFFI6139RPXV](/sequence-files/IGVFFI6139RPXV/), [IGVFFI3305YTLT](/sequence-files/IGVFFI3305YTLT/), [IGVFFI1594NIRL](/sequence-files/IGVFFI1594NIRL/), [IGVFFI1141WNOY](/sequence-files/IGVFFI1141WNOY/), [IGVFFI9286GTIB](/sequence-files/IGVFFI9286GTIB/), [IGVFFI9445WTGW](/sequence-files/IGVFFI9445WTGW/), [IGVFFI7273GVPE](/sequence-files/IGVFFI7273GVPE/), [IGVFFI7031FDMM](/sequence-files/IGVFFI7031FDMM/), [IGVFFI3165SCCW](/sequence-files/IGVFFI3165SCCW/), [IGVFFI2098VOKP](/sequence-files/IGVFFI2098VOKP/), [IGVFFI4643VBFT](/sequence-files/IGVFFI4643VBFT/), [IGVFFI7713CYYJ](/sequence-files/IGVFFI7713CYYJ/), [IGVFFI7231YZOX](/sequence-files/IGVFFI7231YZOX/) 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/IGVFDS4761PXVO/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4761PXVO](/measurement-sets/IGVFDS4761PXVO/) has sequence file(s): [IGVFFI1227JYHU](/sequence-files/IGVFFI1227JYHU/), [IGVFFI0602HGYD](/sequence-files/IGVFFI0602HGYD/), [IGVFFI3716GUMG](/sequence-files/IGVFFI3716GUMG/), [IGVFFI3034OZUL](/sequence-files/IGVFFI3034OZUL/), [IGVFFI7325CDOX](/sequence-files/IGVFFI7325CDOX/), [IGVFFI2191QBIE](/sequence-files/IGVFFI2191QBIE/), [IGVFFI8321VUAU](/sequence-files/IGVFFI8321VUAU/), [IGVFFI4288XHUX](/sequence-files/IGVFFI4288XHUX/), [IGVFFI3808JEKJ](/sequence-files/IGVFFI3808JEKJ/), [IGVFFI7789LABZ](/sequence-files/IGVFFI7789LABZ/), [IGVFFI3933SRWS](/sequence-files/IGVFFI3933SRWS/), [IGVFFI1576FWBE](/sequence-files/IGVFFI1576FWBE/), [IGVFFI6197DOEG](/sequence-files/IGVFFI6197DOEG/), [IGVFFI4927AFPV](/sequence-files/IGVFFI4927AFPV/), [IGVFFI9943RVHV](/sequence-files/IGVFFI9943RVHV/), [IGVFFI6602JMCV](/sequence-files/IGVFFI6602JMCV/), [IGVFFI0030DFFN](/sequence-files/IGVFFI0030DFFN/), [IGVFFI9423LSSX](/sequence-files/IGVFFI9423LSSX/), [IGVFFI1189WLQL](/sequence-files/IGVFFI1189WLQL/), [IGVFFI7066PBGZ](/sequence-files/IGVFFI7066PBGZ/), [IGVFFI5556XSRH](/sequence-files/IGVFFI5556XSRH/), [IGVFFI6629JRKX](/sequence-files/IGVFFI6629JRKX/), [IGVFFI1631MQVE](/sequence-files/IGVFFI1631MQVE/), [IGVFFI5479QUYU](/sequence-files/IGVFFI5479QUYU/), [IGVFFI5561PSUU](/sequence-files/IGVFFI5561PSUU/), [IGVFFI8119ONEN](/sequence-files/IGVFFI8119ONEN/), [IGVFFI7985BQOY](/sequence-files/IGVFFI7985BQOY/), [IGVFFI7638KMFR](/sequence-files/IGVFFI7638KMFR/), [IGVFFI1570DCMH](/sequence-files/IGVFFI1570DCMH/), [IGVFFI5947BHMQ](/sequence-files/IGVFFI5947BHMQ/), [IGVFFI3204GLEE](/sequence-files/IGVFFI3204GLEE/), [IGVFFI3036CLFS](/sequence-files/IGVFFI3036CLFS/), [IGVFFI9131RVAG](/sequence-files/IGVFFI9131RVAG/), [IGVFFI1753ZLCW](/sequence-files/IGVFFI1753ZLCW/), [IGVFFI9671KRGE](/sequence-files/IGVFFI9671KRGE/), [IGVFFI6139RPXV](/sequence-files/IGVFFI6139RPXV/), [IGVFFI3305YTLT](/sequence-files/IGVFFI3305YTLT/), [IGVFFI1594NIRL](/sequence-files/IGVFFI1594NIRL/), [IGVFFI1141WNOY](/sequence-files/IGVFFI1141WNOY/), [IGVFFI9286GTIB](/sequence-files/IGVFFI9286GTIB/), [IGVFFI9445WTGW](/sequence-files/IGVFFI9445WTGW/), [IGVFFI7273GVPE](/sequence-files/IGVFFI7273GVPE/), [IGVFFI7031FDMM](/sequence-files/IGVFFI7031FDMM/), [IGVFFI3165SCCW](/sequence-files/IGVFFI3165SCCW/), [IGVFFI2098VOKP](/sequence-files/IGVFFI2098VOKP/), [IGVFFI4643VBFT](/sequence-files/IGVFFI4643VBFT/), [IGVFFI7713CYYJ](/sequence-files/IGVFFI7713CYYJ/), [IGVFFI7231YZOX](/sequence-files/IGVFFI7231YZOX/) 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/IGVFDS4761PXVO/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM1854TJZA](/in-vitro-systems/IGVFSM1854TJZA/) 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/IGVFSM1854TJZA/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM1854TJZA](/in-vitro-systems/IGVFSM1854TJZA/) 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/IGVFSM1854TJZA/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4761PXVO](/measurement-sets/IGVFDS4761PXVO/) 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/IGVFDS4761PXVO/"
}
]
},
"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": "2023-11-30T22:49:46.601297+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": [
{
"@id": "/sequence-files/IGVFFI1227JYHU/",
"accession": "IGVFFI1227JYHU",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinA-PCRrep9_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:07:05.681017+00:00",
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"file_size": 1810384,
"href": "/sequence-files/IGVFFI1227JYHU/@@download/IGVFFI1227JYHU.fastq.gz",
"md5sum": "b023e7ad5c8436c6de7bc1a9293a0414",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinA-PCRrep9_S153_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0602HGYD/",
"accession": "IGVFFI0602HGYD",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinA-PCRrep12_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:02:44.129353+00:00",
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"file_size": 5846542,
"href": "/sequence-files/IGVFFI0602HGYD/@@download/IGVFFI0602HGYD.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/IGVFFI3716GUMG/",
"accession": "IGVFFI3716GUMG",
"aliases": [
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],
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},
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"upload_status": "validated"
},
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"@id": "/sequence-files/IGVFFI3034OZUL/",
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"aliases": [
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],
"content_type": "reads",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7325CDOX/",
"accession": "IGVFFI7325CDOX",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:03:36.330488+00:00",
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"href": "/sequence-files/IGVFFI7325CDOX/@@download/IGVFFI7325CDOX.fastq.gz",
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"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2191QBIE/",
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"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
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},
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},
{
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],
"content_type": "reads",
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},
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"upload_status": "validated"
},
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"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/IGVFFI3808JEKJ/",
"accession": "IGVFFI3808JEKJ",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:05:39.078941+00:00",
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"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinA-PCRrep6_S150_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7789LABZ/",
"accession": "IGVFFI7789LABZ",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinA-PCRrep7_R2"
],
"content_type": "reads",
"controlled_access": false,
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7231YZOX/",
"accession": "IGVFFI7231YZOX",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinA-PCRrep9_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T21:06:56.984009+00:00",
"file_format": "fastq",
"file_size": 1809357,
"href": "/sequence-files/IGVFFI7231YZOX/@@download/IGVFFI7231YZOX.fastq.gz",
"md5sum": "9fdc9912e2ff24062dbab67bfeac78c3",
"s3_uri": "s3://igvf-files/2023/12/05/5c7a2928-a1d1-4df7-97b8-59e1ef1c29db/IGVFFI7231YZOX.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-BioRep1-FFrep4-BinA-PCRrep9_S153_I1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS3423PSID/"
],
"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": "2023-12-20T23:06:49.873149+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1854TJZA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1854TJZA",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinA"
],
"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 0-25% 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": "2023-12-05T21:00:33.176275+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": "348dc2a3-4973-432a-b319-9f686b2730cd"
}