{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9894YFSM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9894YFSM",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-BinC_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 [IGVFDS9894YFSM](/measurement-sets/IGVFDS9894YFSM/) 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/IGVFDS9894YFSM/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS9894YFSM](/measurement-sets/IGVFDS9894YFSM/) has sequence file(s) [IGVFFI3322HLQW](/sequence-files/IGVFFI3322HLQW/), [IGVFFI0902YQEA](/sequence-files/IGVFFI0902YQEA/), [IGVFFI6140TGXY](/sequence-files/IGVFFI6140TGXY/), [IGVFFI7820KJKQ](/sequence-files/IGVFFI7820KJKQ/), [IGVFFI1129CRIX](/sequence-files/IGVFFI1129CRIX/), [IGVFFI4639MJFW](/sequence-files/IGVFFI4639MJFW/), [IGVFFI9406RBOP](/sequence-files/IGVFFI9406RBOP/), [IGVFFI5617BMIK](/sequence-files/IGVFFI5617BMIK/), [IGVFFI7057XILY](/sequence-files/IGVFFI7057XILY/), [IGVFFI8000WYAL](/sequence-files/IGVFFI8000WYAL/), [IGVFFI5703UDJO](/sequence-files/IGVFFI5703UDJO/), [IGVFFI3076MFPV](/sequence-files/IGVFFI3076MFPV/), [IGVFFI6295SMKM](/sequence-files/IGVFFI6295SMKM/), [IGVFFI6209OOVU](/sequence-files/IGVFFI6209OOVU/), [IGVFFI3722DWKV](/sequence-files/IGVFFI3722DWKV/), [IGVFFI9142OMLY](/sequence-files/IGVFFI9142OMLY/), [IGVFFI9412LAWG](/sequence-files/IGVFFI9412LAWG/), [IGVFFI9822TGGI](/sequence-files/IGVFFI9822TGGI/), [IGVFFI2341DYPQ](/sequence-files/IGVFFI2341DYPQ/), [IGVFFI5922KNSM](/sequence-files/IGVFFI5922KNSM/), [IGVFFI4837QCMR](/sequence-files/IGVFFI4837QCMR/), [IGVFFI6983PSNX](/sequence-files/IGVFFI6983PSNX/), [IGVFFI6830MUSR](/sequence-files/IGVFFI6830MUSR/), [IGVFFI3388PGQI](/sequence-files/IGVFFI3388PGQI/), [IGVFFI1085VHFX](/sequence-files/IGVFFI1085VHFX/), [IGVFFI5109EROK](/sequence-files/IGVFFI5109EROK/), [IGVFFI6361QATP](/sequence-files/IGVFFI6361QATP/), [IGVFFI6622BNIZ](/sequence-files/IGVFFI6622BNIZ/), [IGVFFI4189SNLB](/sequence-files/IGVFFI4189SNLB/), [IGVFFI0364DJME](/sequence-files/IGVFFI0364DJME/), [IGVFFI3045PVZX](/sequence-files/IGVFFI3045PVZX/), [IGVFFI2646BRGL](/sequence-files/IGVFFI2646BRGL/), [IGVFFI8647UTFI](/sequence-files/IGVFFI8647UTFI/), [IGVFFI4232PLMY](/sequence-files/IGVFFI4232PLMY/), [IGVFFI9882QANM](/sequence-files/IGVFFI9882QANM/), [IGVFFI0624DTIF](/sequence-files/IGVFFI0624DTIF/), [IGVFFI0379KPLQ](/sequence-files/IGVFFI0379KPLQ/), [IGVFFI5773HGPZ](/sequence-files/IGVFFI5773HGPZ/), [IGVFFI9520DRPH](/sequence-files/IGVFFI9520DRPH/), [IGVFFI8181AZNK](/sequence-files/IGVFFI8181AZNK/), [IGVFFI2632TWVS](/sequence-files/IGVFFI2632TWVS/), [IGVFFI1708NVIS](/sequence-files/IGVFFI1708NVIS/), [IGVFFI7451UBWP](/sequence-files/IGVFFI7451UBWP/), [IGVFFI0469MIUA](/sequence-files/IGVFFI0469MIUA/), [IGVFFI5450GXWL](/sequence-files/IGVFFI5450GXWL/), [IGVFFI8032BPCP](/sequence-files/IGVFFI8032BPCP/), [IGVFFI7983JOBH](/sequence-files/IGVFFI7983JOBH/), [IGVFFI2968SMHQ](/sequence-files/IGVFFI2968SMHQ/) 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/IGVFDS9894YFSM/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9894YFSM](/measurement-sets/IGVFDS9894YFSM/) has sequence file(s): [IGVFFI3322HLQW](/sequence-files/IGVFFI3322HLQW/), [IGVFFI0902YQEA](/sequence-files/IGVFFI0902YQEA/), [IGVFFI6140TGXY](/sequence-files/IGVFFI6140TGXY/), [IGVFFI7820KJKQ](/sequence-files/IGVFFI7820KJKQ/), [IGVFFI1129CRIX](/sequence-files/IGVFFI1129CRIX/), [IGVFFI4639MJFW](/sequence-files/IGVFFI4639MJFW/), [IGVFFI9406RBOP](/sequence-files/IGVFFI9406RBOP/), [IGVFFI5617BMIK](/sequence-files/IGVFFI5617BMIK/), [IGVFFI7057XILY](/sequence-files/IGVFFI7057XILY/), [IGVFFI8000WYAL](/sequence-files/IGVFFI8000WYAL/), [IGVFFI5703UDJO](/sequence-files/IGVFFI5703UDJO/), [IGVFFI3076MFPV](/sequence-files/IGVFFI3076MFPV/), [IGVFFI6295SMKM](/sequence-files/IGVFFI6295SMKM/), [IGVFFI6209OOVU](/sequence-files/IGVFFI6209OOVU/), [IGVFFI3722DWKV](/sequence-files/IGVFFI3722DWKV/), [IGVFFI9142OMLY](/sequence-files/IGVFFI9142OMLY/), [IGVFFI9412LAWG](/sequence-files/IGVFFI9412LAWG/), [IGVFFI9822TGGI](/sequence-files/IGVFFI9822TGGI/), [IGVFFI2341DYPQ](/sequence-files/IGVFFI2341DYPQ/), [IGVFFI5922KNSM](/sequence-files/IGVFFI5922KNSM/), [IGVFFI4837QCMR](/sequence-files/IGVFFI4837QCMR/), [IGVFFI6983PSNX](/sequence-files/IGVFFI6983PSNX/), [IGVFFI6830MUSR](/sequence-files/IGVFFI6830MUSR/), [IGVFFI3388PGQI](/sequence-files/IGVFFI3388PGQI/), [IGVFFI1085VHFX](/sequence-files/IGVFFI1085VHFX/), [IGVFFI5109EROK](/sequence-files/IGVFFI5109EROK/), [IGVFFI6361QATP](/sequence-files/IGVFFI6361QATP/), [IGVFFI6622BNIZ](/sequence-files/IGVFFI6622BNIZ/), [IGVFFI4189SNLB](/sequence-files/IGVFFI4189SNLB/), [IGVFFI0364DJME](/sequence-files/IGVFFI0364DJME/), [IGVFFI3045PVZX](/sequence-files/IGVFFI3045PVZX/), [IGVFFI2646BRGL](/sequence-files/IGVFFI2646BRGL/), [IGVFFI8647UTFI](/sequence-files/IGVFFI8647UTFI/), [IGVFFI4232PLMY](/sequence-files/IGVFFI4232PLMY/), [IGVFFI9882QANM](/sequence-files/IGVFFI9882QANM/), [IGVFFI0624DTIF](/sequence-files/IGVFFI0624DTIF/), [IGVFFI0379KPLQ](/sequence-files/IGVFFI0379KPLQ/), [IGVFFI5773HGPZ](/sequence-files/IGVFFI5773HGPZ/), [IGVFFI9520DRPH](/sequence-files/IGVFFI9520DRPH/), [IGVFFI8181AZNK](/sequence-files/IGVFFI8181AZNK/), [IGVFFI2632TWVS](/sequence-files/IGVFFI2632TWVS/), [IGVFFI1708NVIS](/sequence-files/IGVFFI1708NVIS/), [IGVFFI7451UBWP](/sequence-files/IGVFFI7451UBWP/), [IGVFFI0469MIUA](/sequence-files/IGVFFI0469MIUA/), [IGVFFI5450GXWL](/sequence-files/IGVFFI5450GXWL/), [IGVFFI8032BPCP](/sequence-files/IGVFFI8032BPCP/), [IGVFFI7983JOBH](/sequence-files/IGVFFI7983JOBH/), [IGVFFI2968SMHQ](/sequence-files/IGVFFI2968SMHQ/) 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/IGVFDS9894YFSM/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM0805ZKDV](/in-vitro-systems/IGVFSM0805ZKDV/) 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/IGVFSM0805ZKDV/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM0805ZKDV](/in-vitro-systems/IGVFSM0805ZKDV/) 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/IGVFSM0805ZKDV/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS9894YFSM](/measurement-sets/IGVFDS9894YFSM/) 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/IGVFDS9894YFSM/"
}
]
},
"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": "2023-11-30T22:49:44.763584+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": "IGVFFI3322HLQW",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-BinC-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:48:30.676484+00:00",
"file_format": "fastq",
"file_size": 1881312,
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"md5sum": "aef64734cde3cac7590bc16c74d647ce",
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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"
},
{
"@id": "/sequence-files/IGVFFI0902YQEA/",
"accession": "IGVFFI0902YQEA",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-BinC-PCRrep3_R1"
],
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"href": "/sequence-files/IGVFFI0902YQEA/@@download/IGVFFI0902YQEA.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/IGVFFI6140TGXY/",
"accession": "IGVFFI6140TGXY",
"aliases": [
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],
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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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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4639MJFW/",
"accession": "IGVFFI4639MJFW",
"aliases": [
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},
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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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"term_name": "Illumina NextSeq 550"
},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8000WYAL/",
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"aliases": [
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],
"content_type": "reads",
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"creation_timestamp": "2023-12-05T20:52:52.263893+00:00",
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"submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-BinC-PCRrep6_S126_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2968SMHQ/",
"accession": "IGVFFI2968SMHQ",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-BinC-PCRrep7_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:51:43.190801+00:00",
"file_format": "fastq",
"file_size": 7116038,
"href": "/sequence-files/IGVFFI2968SMHQ/@@download/IGVFFI2968SMHQ.fastq.gz",
"md5sum": "6d6eafc8acda66744634bc1edf920947",
"s3_uri": "s3://igvf-files/2023/12/05/239af323-a160-44ef-87c6-f2d32b70b430/IGVFFI2968SMHQ.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-FFrep3-BinC-PCRrep7_S127_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": "2023-12-20T23:06:37.106764+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0805ZKDV/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0805ZKDV",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-BinC"
],
"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 51-75% 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": "2023-12-05T20:46:02.563918+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": "1e3b0562-032a-4599-9ea6-6e60fca191ee"
}