{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4750CFGI/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4750CFGI",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinD_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 [IGVFDS4750CFGI](/measurement-sets/IGVFDS4750CFGI/) 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/IGVFDS4750CFGI/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS4750CFGI](/measurement-sets/IGVFDS4750CFGI/) has sequence file(s) [IGVFFI6255HXFA](/sequence-files/IGVFFI6255HXFA/), [IGVFFI3525KPXA](/sequence-files/IGVFFI3525KPXA/), [IGVFFI7418EQZO](/sequence-files/IGVFFI7418EQZO/), [IGVFFI8579JNHK](/sequence-files/IGVFFI8579JNHK/), [IGVFFI1115HRCH](/sequence-files/IGVFFI1115HRCH/), [IGVFFI3730VWQZ](/sequence-files/IGVFFI3730VWQZ/), [IGVFFI3577ZQHN](/sequence-files/IGVFFI3577ZQHN/), [IGVFFI4170VBYF](/sequence-files/IGVFFI4170VBYF/), [IGVFFI1642FLWS](/sequence-files/IGVFFI1642FLWS/), [IGVFFI4763RXBN](/sequence-files/IGVFFI4763RXBN/), [IGVFFI9959POCM](/sequence-files/IGVFFI9959POCM/), [IGVFFI6364ENDE](/sequence-files/IGVFFI6364ENDE/), [IGVFFI2093UXGZ](/sequence-files/IGVFFI2093UXGZ/), [IGVFFI4910IQKO](/sequence-files/IGVFFI4910IQKO/), [IGVFFI3287DJCQ](/sequence-files/IGVFFI3287DJCQ/), [IGVFFI8306IKIS](/sequence-files/IGVFFI8306IKIS/), [IGVFFI5577RNVG](/sequence-files/IGVFFI5577RNVG/), [IGVFFI8433IPFN](/sequence-files/IGVFFI8433IPFN/), [IGVFFI4681RKIY](/sequence-files/IGVFFI4681RKIY/), [IGVFFI9374AVTV](/sequence-files/IGVFFI9374AVTV/), [IGVFFI2890FTTC](/sequence-files/IGVFFI2890FTTC/), [IGVFFI6616SPDM](/sequence-files/IGVFFI6616SPDM/), [IGVFFI3455QRIN](/sequence-files/IGVFFI3455QRIN/), [IGVFFI9659AERT](/sequence-files/IGVFFI9659AERT/), [IGVFFI7226XSRT](/sequence-files/IGVFFI7226XSRT/), [IGVFFI4569JLJK](/sequence-files/IGVFFI4569JLJK/), [IGVFFI7549MQAH](/sequence-files/IGVFFI7549MQAH/), [IGVFFI0075VJGZ](/sequence-files/IGVFFI0075VJGZ/), [IGVFFI7609BEAO](/sequence-files/IGVFFI7609BEAO/), [IGVFFI0828MUJH](/sequence-files/IGVFFI0828MUJH/), [IGVFFI9878TIHC](/sequence-files/IGVFFI9878TIHC/), [IGVFFI5780LOEX](/sequence-files/IGVFFI5780LOEX/), [IGVFFI3682QYMT](/sequence-files/IGVFFI3682QYMT/), [IGVFFI1543OVLR](/sequence-files/IGVFFI1543OVLR/), [IGVFFI4912GFBI](/sequence-files/IGVFFI4912GFBI/), [IGVFFI4159UMTQ](/sequence-files/IGVFFI4159UMTQ/), [IGVFFI9446BKUO](/sequence-files/IGVFFI9446BKUO/), [IGVFFI8566WGAZ](/sequence-files/IGVFFI8566WGAZ/), [IGVFFI7439IGNL](/sequence-files/IGVFFI7439IGNL/), [IGVFFI6061FDON](/sequence-files/IGVFFI6061FDON/), [IGVFFI0624UPKR](/sequence-files/IGVFFI0624UPKR/), [IGVFFI9408PUTF](/sequence-files/IGVFFI9408PUTF/), [IGVFFI2453RRBK](/sequence-files/IGVFFI2453RRBK/), [IGVFFI1475IAAT](/sequence-files/IGVFFI1475IAAT/), [IGVFFI8654UEHF](/sequence-files/IGVFFI8654UEHF/), [IGVFFI2355REZW](/sequence-files/IGVFFI2355REZW/), [IGVFFI0636GZHN](/sequence-files/IGVFFI0636GZHN/), [IGVFFI9514NCEA](/sequence-files/IGVFFI9514NCEA/) 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/IGVFDS4750CFGI/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4750CFGI](/measurement-sets/IGVFDS4750CFGI/) has sequence file(s): [IGVFFI6255HXFA](/sequence-files/IGVFFI6255HXFA/), [IGVFFI3525KPXA](/sequence-files/IGVFFI3525KPXA/), [IGVFFI7418EQZO](/sequence-files/IGVFFI7418EQZO/), [IGVFFI8579JNHK](/sequence-files/IGVFFI8579JNHK/), [IGVFFI1115HRCH](/sequence-files/IGVFFI1115HRCH/), [IGVFFI3730VWQZ](/sequence-files/IGVFFI3730VWQZ/), [IGVFFI3577ZQHN](/sequence-files/IGVFFI3577ZQHN/), [IGVFFI4170VBYF](/sequence-files/IGVFFI4170VBYF/), [IGVFFI1642FLWS](/sequence-files/IGVFFI1642FLWS/), [IGVFFI4763RXBN](/sequence-files/IGVFFI4763RXBN/), [IGVFFI9959POCM](/sequence-files/IGVFFI9959POCM/), [IGVFFI6364ENDE](/sequence-files/IGVFFI6364ENDE/), [IGVFFI2093UXGZ](/sequence-files/IGVFFI2093UXGZ/), [IGVFFI4910IQKO](/sequence-files/IGVFFI4910IQKO/), [IGVFFI3287DJCQ](/sequence-files/IGVFFI3287DJCQ/), [IGVFFI8306IKIS](/sequence-files/IGVFFI8306IKIS/), [IGVFFI5577RNVG](/sequence-files/IGVFFI5577RNVG/), [IGVFFI8433IPFN](/sequence-files/IGVFFI8433IPFN/), [IGVFFI4681RKIY](/sequence-files/IGVFFI4681RKIY/), [IGVFFI9374AVTV](/sequence-files/IGVFFI9374AVTV/), [IGVFFI2890FTTC](/sequence-files/IGVFFI2890FTTC/), [IGVFFI6616SPDM](/sequence-files/IGVFFI6616SPDM/), [IGVFFI3455QRIN](/sequence-files/IGVFFI3455QRIN/), [IGVFFI9659AERT](/sequence-files/IGVFFI9659AERT/), [IGVFFI7226XSRT](/sequence-files/IGVFFI7226XSRT/), [IGVFFI4569JLJK](/sequence-files/IGVFFI4569JLJK/), [IGVFFI7549MQAH](/sequence-files/IGVFFI7549MQAH/), [IGVFFI0075VJGZ](/sequence-files/IGVFFI0075VJGZ/), [IGVFFI7609BEAO](/sequence-files/IGVFFI7609BEAO/), [IGVFFI0828MUJH](/sequence-files/IGVFFI0828MUJH/), [IGVFFI9878TIHC](/sequence-files/IGVFFI9878TIHC/), [IGVFFI5780LOEX](/sequence-files/IGVFFI5780LOEX/), [IGVFFI3682QYMT](/sequence-files/IGVFFI3682QYMT/), [IGVFFI1543OVLR](/sequence-files/IGVFFI1543OVLR/), [IGVFFI4912GFBI](/sequence-files/IGVFFI4912GFBI/), [IGVFFI4159UMTQ](/sequence-files/IGVFFI4159UMTQ/), [IGVFFI9446BKUO](/sequence-files/IGVFFI9446BKUO/), [IGVFFI8566WGAZ](/sequence-files/IGVFFI8566WGAZ/), [IGVFFI7439IGNL](/sequence-files/IGVFFI7439IGNL/), [IGVFFI6061FDON](/sequence-files/IGVFFI6061FDON/), [IGVFFI0624UPKR](/sequence-files/IGVFFI0624UPKR/), [IGVFFI9408PUTF](/sequence-files/IGVFFI9408PUTF/), [IGVFFI2453RRBK](/sequence-files/IGVFFI2453RRBK/), [IGVFFI1475IAAT](/sequence-files/IGVFFI1475IAAT/), [IGVFFI8654UEHF](/sequence-files/IGVFFI8654UEHF/), [IGVFFI2355REZW](/sequence-files/IGVFFI2355REZW/), [IGVFFI0636GZHN](/sequence-files/IGVFFI0636GZHN/), [IGVFFI9514NCEA](/sequence-files/IGVFFI9514NCEA/) 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/IGVFDS4750CFGI/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM2674RBOA](/in-vitro-systems/IGVFSM2674RBOA/) 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/IGVFSM2674RBOA/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM2674RBOA](/in-vitro-systems/IGVFSM2674RBOA/) 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/IGVFSM2674RBOA/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4750CFGI](/measurement-sets/IGVFDS4750CFGI/) 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/IGVFDS4750CFGI/"
}
]
},
"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": "2023-11-30T22:50:01.885962+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": "IGVFFI6255HXFA",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinD-PCRrep7_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:28:31.587844+00:00",
"file_format": "fastq",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
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"accession": "IGVFFI3525KPXA",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinD-PCRrep12_I1"
],
"content_type": "reads",
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"creation_timestamp": "2023-12-05T22:24:35.849764+00:00",
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"status": "released",
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7418EQZO/",
"accession": "IGVFFI7418EQZO",
"aliases": [
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],
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},
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"aliases": [
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],
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1115HRCH/",
"accession": "IGVFFI1115HRCH",
"aliases": [
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},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3730VWQZ/",
"accession": "IGVFFI3730VWQZ",
"aliases": [
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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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"aliases": [
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],
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},
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"upload_status": "validated"
},
{
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"aliases": [
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],
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4763RXBN/",
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"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:23:26.126935+00:00",
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"accession": "IGVFFI9514NCEA",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinD-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T22:23:17.460782+00:00",
"file_format": "fastq",
"file_size": 4840396,
"href": "/sequence-files/IGVFFI9514NCEA/@@download/IGVFFI9514NCEA.fastq.gz",
"md5sum": "233faf9b1aaad62075c70bc9ba21c9f9",
"s3_uri": "s3://igvf-files/2023/12/05/e287045c-b142-45d1-a838-f2d6fed0b4e5/IGVFFI9514NCEA.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-BinD-PCRrep1_S277_R2_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": "2023-12-20T23:05:17.318294+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2674RBOA/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2674RBOA",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinD"
],
"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 76-100% 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": "2023-12-05T22:22:51.467660+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": "594f18f0-565a-48b7-b1d0-3788b9552541"
}