{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8290UELV/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8290UELV",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep2-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 [IGVFDS8290UELV](/measurement-sets/IGVFDS8290UELV/) 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/IGVFDS8290UELV/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS8290UELV](/measurement-sets/IGVFDS8290UELV/) has sequence file(s) [IGVFFI2254VOYD](/sequence-files/IGVFFI2254VOYD/), [IGVFFI7142VXQK](/sequence-files/IGVFFI7142VXQK/), [IGVFFI1408JDPQ](/sequence-files/IGVFFI1408JDPQ/), [IGVFFI9896MTMM](/sequence-files/IGVFFI9896MTMM/), [IGVFFI5563JMHV](/sequence-files/IGVFFI5563JMHV/), [IGVFFI0387FPMY](/sequence-files/IGVFFI0387FPMY/), [IGVFFI4138AATQ](/sequence-files/IGVFFI4138AATQ/), [IGVFFI4493TOBA](/sequence-files/IGVFFI4493TOBA/), [IGVFFI5534WCUN](/sequence-files/IGVFFI5534WCUN/), [IGVFFI8679WTBT](/sequence-files/IGVFFI8679WTBT/), [IGVFFI6438NOMG](/sequence-files/IGVFFI6438NOMG/), [IGVFFI2422ZKZB](/sequence-files/IGVFFI2422ZKZB/), [IGVFFI3711INTE](/sequence-files/IGVFFI3711INTE/), [IGVFFI3756DIIQ](/sequence-files/IGVFFI3756DIIQ/), [IGVFFI8961QBBH](/sequence-files/IGVFFI8961QBBH/), [IGVFFI7379YHHE](/sequence-files/IGVFFI7379YHHE/), [IGVFFI4646AFOE](/sequence-files/IGVFFI4646AFOE/), [IGVFFI9579VQHA](/sequence-files/IGVFFI9579VQHA/), [IGVFFI5455OVIW](/sequence-files/IGVFFI5455OVIW/), [IGVFFI5790PHLD](/sequence-files/IGVFFI5790PHLD/), [IGVFFI7053STAC](/sequence-files/IGVFFI7053STAC/), [IGVFFI8367TBRE](/sequence-files/IGVFFI8367TBRE/), [IGVFFI2573VODS](/sequence-files/IGVFFI2573VODS/), [IGVFFI7167RQIU](/sequence-files/IGVFFI7167RQIU/), [IGVFFI5844IKPT](/sequence-files/IGVFFI5844IKPT/), [IGVFFI6387FJAI](/sequence-files/IGVFFI6387FJAI/), [IGVFFI3573SDZR](/sequence-files/IGVFFI3573SDZR/), [IGVFFI5708AATE](/sequence-files/IGVFFI5708AATE/), [IGVFFI5825DFPV](/sequence-files/IGVFFI5825DFPV/), [IGVFFI4256UIEM](/sequence-files/IGVFFI4256UIEM/), [IGVFFI1506SUZB](/sequence-files/IGVFFI1506SUZB/), [IGVFFI8407DPZK](/sequence-files/IGVFFI8407DPZK/), [IGVFFI5313UFBQ](/sequence-files/IGVFFI5313UFBQ/), [IGVFFI5650WUTD](/sequence-files/IGVFFI5650WUTD/), [IGVFFI8357ZIGB](/sequence-files/IGVFFI8357ZIGB/), [IGVFFI1482QPDO](/sequence-files/IGVFFI1482QPDO/), [IGVFFI6262TWNO](/sequence-files/IGVFFI6262TWNO/), [IGVFFI9981REPA](/sequence-files/IGVFFI9981REPA/), [IGVFFI0871VENP](/sequence-files/IGVFFI0871VENP/), [IGVFFI7204DTUT](/sequence-files/IGVFFI7204DTUT/), [IGVFFI9303RDNK](/sequence-files/IGVFFI9303RDNK/), [IGVFFI9925SQCB](/sequence-files/IGVFFI9925SQCB/), [IGVFFI3956TKGN](/sequence-files/IGVFFI3956TKGN/), [IGVFFI1792KQZA](/sequence-files/IGVFFI1792KQZA/), [IGVFFI1787XWYQ](/sequence-files/IGVFFI1787XWYQ/), [IGVFFI2323LRJO](/sequence-files/IGVFFI2323LRJO/), [IGVFFI2453XRKJ](/sequence-files/IGVFFI2453XRKJ/), [IGVFFI2751LAKD](/sequence-files/IGVFFI2751LAKD/) 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/IGVFDS8290UELV/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8290UELV](/measurement-sets/IGVFDS8290UELV/) has sequence file(s): [IGVFFI2254VOYD](/sequence-files/IGVFFI2254VOYD/), [IGVFFI7142VXQK](/sequence-files/IGVFFI7142VXQK/), [IGVFFI1408JDPQ](/sequence-files/IGVFFI1408JDPQ/), [IGVFFI9896MTMM](/sequence-files/IGVFFI9896MTMM/), [IGVFFI5563JMHV](/sequence-files/IGVFFI5563JMHV/), [IGVFFI0387FPMY](/sequence-files/IGVFFI0387FPMY/), [IGVFFI4138AATQ](/sequence-files/IGVFFI4138AATQ/), [IGVFFI4493TOBA](/sequence-files/IGVFFI4493TOBA/), [IGVFFI5534WCUN](/sequence-files/IGVFFI5534WCUN/), [IGVFFI8679WTBT](/sequence-files/IGVFFI8679WTBT/), [IGVFFI6438NOMG](/sequence-files/IGVFFI6438NOMG/), [IGVFFI2422ZKZB](/sequence-files/IGVFFI2422ZKZB/), [IGVFFI3711INTE](/sequence-files/IGVFFI3711INTE/), [IGVFFI3756DIIQ](/sequence-files/IGVFFI3756DIIQ/), [IGVFFI8961QBBH](/sequence-files/IGVFFI8961QBBH/), [IGVFFI7379YHHE](/sequence-files/IGVFFI7379YHHE/), [IGVFFI4646AFOE](/sequence-files/IGVFFI4646AFOE/), [IGVFFI9579VQHA](/sequence-files/IGVFFI9579VQHA/), [IGVFFI5455OVIW](/sequence-files/IGVFFI5455OVIW/), [IGVFFI5790PHLD](/sequence-files/IGVFFI5790PHLD/), [IGVFFI7053STAC](/sequence-files/IGVFFI7053STAC/), [IGVFFI8367TBRE](/sequence-files/IGVFFI8367TBRE/), [IGVFFI2573VODS](/sequence-files/IGVFFI2573VODS/), [IGVFFI7167RQIU](/sequence-files/IGVFFI7167RQIU/), [IGVFFI5844IKPT](/sequence-files/IGVFFI5844IKPT/), [IGVFFI6387FJAI](/sequence-files/IGVFFI6387FJAI/), [IGVFFI3573SDZR](/sequence-files/IGVFFI3573SDZR/), [IGVFFI5708AATE](/sequence-files/IGVFFI5708AATE/), [IGVFFI5825DFPV](/sequence-files/IGVFFI5825DFPV/), [IGVFFI4256UIEM](/sequence-files/IGVFFI4256UIEM/), [IGVFFI1506SUZB](/sequence-files/IGVFFI1506SUZB/), [IGVFFI8407DPZK](/sequence-files/IGVFFI8407DPZK/), [IGVFFI5313UFBQ](/sequence-files/IGVFFI5313UFBQ/), [IGVFFI5650WUTD](/sequence-files/IGVFFI5650WUTD/), [IGVFFI8357ZIGB](/sequence-files/IGVFFI8357ZIGB/), [IGVFFI1482QPDO](/sequence-files/IGVFFI1482QPDO/), [IGVFFI6262TWNO](/sequence-files/IGVFFI6262TWNO/), [IGVFFI9981REPA](/sequence-files/IGVFFI9981REPA/), [IGVFFI0871VENP](/sequence-files/IGVFFI0871VENP/), [IGVFFI7204DTUT](/sequence-files/IGVFFI7204DTUT/), [IGVFFI9303RDNK](/sequence-files/IGVFFI9303RDNK/), [IGVFFI9925SQCB](/sequence-files/IGVFFI9925SQCB/), [IGVFFI3956TKGN](/sequence-files/IGVFFI3956TKGN/), [IGVFFI1792KQZA](/sequence-files/IGVFFI1792KQZA/), [IGVFFI1787XWYQ](/sequence-files/IGVFFI1787XWYQ/), [IGVFFI2323LRJO](/sequence-files/IGVFFI2323LRJO/), [IGVFFI2453XRKJ](/sequence-files/IGVFFI2453XRKJ/), [IGVFFI2751LAKD](/sequence-files/IGVFFI2751LAKD/) 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/IGVFDS8290UELV/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM3965ATNS](/in-vitro-systems/IGVFSM3965ATNS/) 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/IGVFSM3965ATNS/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM3965ATNS](/in-vitro-systems/IGVFSM3965ATNS/) 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/IGVFSM3965ATNS/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS8290UELV](/measurement-sets/IGVFDS8290UELV/) 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/IGVFDS8290UELV/"
}
]
},
"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": "2023-11-30T22:49:35.873182+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/IGVFFI2254VOYD/",
"accession": "IGVFFI2254VOYD",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
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"term_name": "Illumina NextSeq 550"
},
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"upload_status": "validated"
},
{
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"accession": "IGVFFI7142VXQK",
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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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},
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],
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},
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"upload_status": "validated"
},
{
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],
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"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep2-BinA-PCRrep10_S58_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2751LAKD/",
"accession": "IGVFFI2751LAKD",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep2-BinA-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:00:56.464123+00:00",
"file_format": "fastq",
"file_size": 7776784,
"href": "/sequence-files/IGVFFI2751LAKD/@@download/IGVFFI2751LAKD.fastq.gz",
"md5sum": "9a3c4e1eb87340fe88f8ee9e1b475d9a",
"s3_uri": "s3://igvf-files/2023/12/05/b2fc74e6-a221-45e9-bcac-dff1f1c85785/IGVFFI2751LAKD.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-FFrep2-BinA-PCRrep2_S50_R1_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": "2023-12-20T23:06:23.357584+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3965ATNS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3965ATNS",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep2-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": "2023-12-05T19:58:15.742383+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": "a9e4b271-8c21-4db5-953d-8dde501e73a8"
}