{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7230BLHQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7230BLHQ",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-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 [IGVFDS7230BLHQ](/measurement-sets/IGVFDS7230BLHQ/) 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/IGVFDS7230BLHQ/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS7230BLHQ](/measurement-sets/IGVFDS7230BLHQ/) has sequence file(s) [IGVFFI0828GBKP](/sequence-files/IGVFFI0828GBKP/), [IGVFFI8691CGWZ](/sequence-files/IGVFFI8691CGWZ/), [IGVFFI4478NNIT](/sequence-files/IGVFFI4478NNIT/), [IGVFFI2554OKGO](/sequence-files/IGVFFI2554OKGO/), [IGVFFI3018JCKY](/sequence-files/IGVFFI3018JCKY/), [IGVFFI5568NHOM](/sequence-files/IGVFFI5568NHOM/), [IGVFFI6683SEMP](/sequence-files/IGVFFI6683SEMP/), [IGVFFI3780QQEF](/sequence-files/IGVFFI3780QQEF/), [IGVFFI8932HREH](/sequence-files/IGVFFI8932HREH/), [IGVFFI5443JJRM](/sequence-files/IGVFFI5443JJRM/), [IGVFFI1211SHRN](/sequence-files/IGVFFI1211SHRN/), [IGVFFI9041WFPI](/sequence-files/IGVFFI9041WFPI/), [IGVFFI3103OOAW](/sequence-files/IGVFFI3103OOAW/), [IGVFFI1548OKBK](/sequence-files/IGVFFI1548OKBK/), [IGVFFI1189YXEX](/sequence-files/IGVFFI1189YXEX/), [IGVFFI0834IRPD](/sequence-files/IGVFFI0834IRPD/), [IGVFFI1383QEVT](/sequence-files/IGVFFI1383QEVT/), [IGVFFI4183QZRA](/sequence-files/IGVFFI4183QZRA/), [IGVFFI4942JEVM](/sequence-files/IGVFFI4942JEVM/), [IGVFFI7396UAFJ](/sequence-files/IGVFFI7396UAFJ/), [IGVFFI4568MRKN](/sequence-files/IGVFFI4568MRKN/), [IGVFFI1405ACUB](/sequence-files/IGVFFI1405ACUB/), [IGVFFI0791ISZY](/sequence-files/IGVFFI0791ISZY/), [IGVFFI5420SZFO](/sequence-files/IGVFFI5420SZFO/), [IGVFFI9249MZDZ](/sequence-files/IGVFFI9249MZDZ/), [IGVFFI9587PZUS](/sequence-files/IGVFFI9587PZUS/), [IGVFFI5069ZDRK](/sequence-files/IGVFFI5069ZDRK/), [IGVFFI0774UBYU](/sequence-files/IGVFFI0774UBYU/), [IGVFFI3229UPHU](/sequence-files/IGVFFI3229UPHU/), [IGVFFI1911VRNA](/sequence-files/IGVFFI1911VRNA/), [IGVFFI9692NMWH](/sequence-files/IGVFFI9692NMWH/), [IGVFFI4300WRZM](/sequence-files/IGVFFI4300WRZM/), [IGVFFI3161IUGU](/sequence-files/IGVFFI3161IUGU/), [IGVFFI4241NIAE](/sequence-files/IGVFFI4241NIAE/), [IGVFFI9837BABJ](/sequence-files/IGVFFI9837BABJ/), [IGVFFI1853ENRS](/sequence-files/IGVFFI1853ENRS/), [IGVFFI8112PCYM](/sequence-files/IGVFFI8112PCYM/), [IGVFFI6519TGSS](/sequence-files/IGVFFI6519TGSS/), [IGVFFI6960TVYM](/sequence-files/IGVFFI6960TVYM/), [IGVFFI6831UJXI](/sequence-files/IGVFFI6831UJXI/), [IGVFFI7879KRNU](/sequence-files/IGVFFI7879KRNU/), [IGVFFI8661YNZJ](/sequence-files/IGVFFI8661YNZJ/), [IGVFFI4132FUOU](/sequence-files/IGVFFI4132FUOU/), [IGVFFI2286UMKC](/sequence-files/IGVFFI2286UMKC/), [IGVFFI0349KYPZ](/sequence-files/IGVFFI0349KYPZ/), [IGVFFI9969JHKS](/sequence-files/IGVFFI9969JHKS/), [IGVFFI6315SSRO](/sequence-files/IGVFFI6315SSRO/), [IGVFFI5900QSIY](/sequence-files/IGVFFI5900QSIY/) 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/IGVFDS7230BLHQ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7230BLHQ](/measurement-sets/IGVFDS7230BLHQ/) has sequence file(s): [IGVFFI0828GBKP](/sequence-files/IGVFFI0828GBKP/), [IGVFFI8691CGWZ](/sequence-files/IGVFFI8691CGWZ/), [IGVFFI4478NNIT](/sequence-files/IGVFFI4478NNIT/), [IGVFFI2554OKGO](/sequence-files/IGVFFI2554OKGO/), [IGVFFI3018JCKY](/sequence-files/IGVFFI3018JCKY/), [IGVFFI5568NHOM](/sequence-files/IGVFFI5568NHOM/), [IGVFFI6683SEMP](/sequence-files/IGVFFI6683SEMP/), [IGVFFI3780QQEF](/sequence-files/IGVFFI3780QQEF/), [IGVFFI8932HREH](/sequence-files/IGVFFI8932HREH/), [IGVFFI5443JJRM](/sequence-files/IGVFFI5443JJRM/), [IGVFFI1211SHRN](/sequence-files/IGVFFI1211SHRN/), [IGVFFI9041WFPI](/sequence-files/IGVFFI9041WFPI/), [IGVFFI3103OOAW](/sequence-files/IGVFFI3103OOAW/), [IGVFFI1548OKBK](/sequence-files/IGVFFI1548OKBK/), [IGVFFI1189YXEX](/sequence-files/IGVFFI1189YXEX/), [IGVFFI0834IRPD](/sequence-files/IGVFFI0834IRPD/), [IGVFFI1383QEVT](/sequence-files/IGVFFI1383QEVT/), [IGVFFI4183QZRA](/sequence-files/IGVFFI4183QZRA/), [IGVFFI4942JEVM](/sequence-files/IGVFFI4942JEVM/), [IGVFFI7396UAFJ](/sequence-files/IGVFFI7396UAFJ/), [IGVFFI4568MRKN](/sequence-files/IGVFFI4568MRKN/), [IGVFFI1405ACUB](/sequence-files/IGVFFI1405ACUB/), [IGVFFI0791ISZY](/sequence-files/IGVFFI0791ISZY/), [IGVFFI5420SZFO](/sequence-files/IGVFFI5420SZFO/), [IGVFFI9249MZDZ](/sequence-files/IGVFFI9249MZDZ/), [IGVFFI9587PZUS](/sequence-files/IGVFFI9587PZUS/), [IGVFFI5069ZDRK](/sequence-files/IGVFFI5069ZDRK/), [IGVFFI0774UBYU](/sequence-files/IGVFFI0774UBYU/), [IGVFFI3229UPHU](/sequence-files/IGVFFI3229UPHU/), [IGVFFI1911VRNA](/sequence-files/IGVFFI1911VRNA/), [IGVFFI9692NMWH](/sequence-files/IGVFFI9692NMWH/), [IGVFFI4300WRZM](/sequence-files/IGVFFI4300WRZM/), [IGVFFI3161IUGU](/sequence-files/IGVFFI3161IUGU/), [IGVFFI4241NIAE](/sequence-files/IGVFFI4241NIAE/), [IGVFFI9837BABJ](/sequence-files/IGVFFI9837BABJ/), [IGVFFI1853ENRS](/sequence-files/IGVFFI1853ENRS/), [IGVFFI8112PCYM](/sequence-files/IGVFFI8112PCYM/), [IGVFFI6519TGSS](/sequence-files/IGVFFI6519TGSS/), [IGVFFI6960TVYM](/sequence-files/IGVFFI6960TVYM/), [IGVFFI6831UJXI](/sequence-files/IGVFFI6831UJXI/), [IGVFFI7879KRNU](/sequence-files/IGVFFI7879KRNU/), [IGVFFI8661YNZJ](/sequence-files/IGVFFI8661YNZJ/), [IGVFFI4132FUOU](/sequence-files/IGVFFI4132FUOU/), [IGVFFI2286UMKC](/sequence-files/IGVFFI2286UMKC/), [IGVFFI0349KYPZ](/sequence-files/IGVFFI0349KYPZ/), [IGVFFI9969JHKS](/sequence-files/IGVFFI9969JHKS/), [IGVFFI6315SSRO](/sequence-files/IGVFFI6315SSRO/), [IGVFFI5900QSIY](/sequence-files/IGVFFI5900QSIY/) 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/IGVFDS7230BLHQ/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM6168MZCU](/in-vitro-systems/IGVFSM6168MZCU/) has in progress subobject construct library set [IGVFDS2385DHZO](/construct-library-sets/IGVFDS2385DHZO/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM6168MZCU/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM6168MZCU](/in-vitro-systems/IGVFSM6168MZCU/) 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/IGVFSM6168MZCU/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7230BLHQ](/measurement-sets/IGVFDS7230BLHQ/) 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/IGVFDS7230BLHQ/"
}
]
},
"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/IGVFDS2385DHZO/",
"accession": "IGVFDS2385DHZO",
"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/IGVFDS5128CXIS/",
"accession": "IGVFDS5128CXIS",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"creation_timestamp": "2023-12-13T08:01:40.873960+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": "IGVFFI0828GBKP",
"aliases": [
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"content_type": "reads",
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"creation_timestamp": "2023-12-13T09:46:58.072380+00:00",
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"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8691CGWZ/",
"accession": "IGVFFI8691CGWZ",
"aliases": [
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],
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"creation_timestamp": "2023-12-13T15:22:45.584863+00:00",
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},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4478NNIT/",
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},
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3018JCKY/",
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"aliases": [
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},
"status": "released",
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"upload_status": "validated"
},
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"@id": "/sequence-files/IGVFFI5568NHOM/",
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],
"content_type": "reads",
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},
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"upload_status": "validated"
},
{
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},
"status": "released",
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"upload_status": "validated"
},
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},
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},
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"@id": "/sequence-files/IGVFFI8932HREH/",
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"aliases": [
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],
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"controlled_access": false,
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5443JJRM/",
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"aliases": [
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],
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"submitted_file_name": "230523pPPIFEnformerTHP1-THP1-PE-pPPIF_Enformer-Amp-pPPIF-BioRep1-FFRep3_BinD-PCRrep10_S142_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6315SSRO/",
"accession": "IGVFFI6315SSRO",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-BinD-PCRrep12_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T16:27:44.100824+00:00",
"file_format": "fastq",
"file_size": 2613084,
"href": "/sequence-files/IGVFFI6315SSRO/@@download/IGVFFI6315SSRO.fastq.gz",
"md5sum": "8ea81caaeeb61360c9c6f75b6fd38d0c",
"s3_uri": "s3://igvf-files/2023/12/13/fe9acede-4a4a-494f-8330-a8aa54c9e06f/IGVFFI6315SSRO.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230523pPPIFEnformerTHP1-THP1-PE-pPPIF_Enformer-Amp-pPPIF-BioRep1-FFRep3_BinD-PCRrep12_S144_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5900QSIY/",
"accession": "IGVFFI5900QSIY",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-BinD-PCRrep9_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-13T08:39:49.680099+00:00",
"file_format": "fastq",
"file_size": 12430472,
"href": "/sequence-files/IGVFFI5900QSIY/@@download/IGVFFI5900QSIY.fastq.gz",
"md5sum": "c03530fd502b6856b712a459925075c1",
"s3_uri": "s3://igvf-files/2023/12/13/bf57ccba-b6ed-4526-ba5d-846563d9c6d3/IGVFFI5900QSIY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "230523pPPIFEnformerTHP1-THP1-PE-pPPIF_Enformer-Amp-pPPIF-BioRep1-FFRep3_BinD-PCRrep9_S141_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4359OODY/"
],
"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": "2023-12-20T23:07:45.630768+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6168MZCU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6168MZCU",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-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": "2023-12-13T08:34:03.773634+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": "242fa861-26ee-4d22-8c74-8e05426aafd6"
}