{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0839SQRJ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0839SQRJ",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep3-BinC_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM0890ULSF](/in-vitro-systems/IGVFSM0890ULSF/) 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/IGVFSM0890ULSF/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0839SQRJ](/measurement-sets/IGVFDS0839SQRJ/) has in progress subobject auxiliary set [IGVFDS7100TFDB](/auxiliary-sets/IGVFDS7100TFDB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0839SQRJ/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS7100TFDB](/auxiliary-sets/IGVFDS7100TFDB/) has sequence file(s): [IGVFFI5357MXXH](/sequence-files/IGVFFI5357MXXH/), [IGVFFI6093YBAZ](/sequence-files/IGVFFI6093YBAZ/), [IGVFFI6611WMMZ](/sequence-files/IGVFFI6611WMMZ/), [IGVFFI5582FKUS](/sequence-files/IGVFFI5582FKUS/), [IGVFFI5683NIXR](/sequence-files/IGVFFI5683NIXR/), [IGVFFI0318GWBO](/sequence-files/IGVFFI0318GWBO/), [IGVFFI5176UXJE](/sequence-files/IGVFFI5176UXJE/), [IGVFFI3398EYGW](/sequence-files/IGVFFI3398EYGW/), [IGVFFI1028LFBE](/sequence-files/IGVFFI1028LFBE/), [IGVFFI4337UZYQ](/sequence-files/IGVFFI4337UZYQ/), [IGVFFI1594RLYS](/sequence-files/IGVFFI1594RLYS/), [IGVFFI2394UNNV](/sequence-files/IGVFFI2394UNNV/), [IGVFFI3311DACT](/sequence-files/IGVFFI3311DACT/), [IGVFFI4377YQQR](/sequence-files/IGVFFI4377YQQR/), [IGVFFI3739XFPS](/sequence-files/IGVFFI3739XFPS/), [IGVFFI4630DQJD](/sequence-files/IGVFFI4630DQJD/), [IGVFFI7130VZAO](/sequence-files/IGVFFI7130VZAO/), [IGVFFI4885ANSD](/sequence-files/IGVFFI4885ANSD/), [IGVFFI6370OHKN](/sequence-files/IGVFFI6370OHKN/), [IGVFFI2899LEMP](/sequence-files/IGVFFI2899LEMP/), [IGVFFI0501JGMG](/sequence-files/IGVFFI0501JGMG/), [IGVFFI4436PDOZ](/sequence-files/IGVFFI4436PDOZ/), [IGVFFI3562UGCX](/sequence-files/IGVFFI3562UGCX/), [IGVFFI3683VWLI](/sequence-files/IGVFFI3683VWLI/), [IGVFFI2613DCAO](/sequence-files/IGVFFI2613DCAO/), [IGVFFI0794PHCL](/sequence-files/IGVFFI0794PHCL/), [IGVFFI0242JSKB](/sequence-files/IGVFFI0242JSKB/), [IGVFFI3070RDZQ](/sequence-files/IGVFFI3070RDZQ/), [IGVFFI1118EWBM](/sequence-files/IGVFFI1118EWBM/), [IGVFFI8301AKCU](/sequence-files/IGVFFI8301AKCU/), [IGVFFI2441TLMB](/sequence-files/IGVFFI2441TLMB/), [IGVFFI8770XIYP](/sequence-files/IGVFFI8770XIYP/), [IGVFFI8601GRVM](/sequence-files/IGVFFI8601GRVM/), [IGVFFI7795QKJJ](/sequence-files/IGVFFI7795QKJJ/), [IGVFFI9740OJZC](/sequence-files/IGVFFI9740OJZC/), [IGVFFI6226NROV](/sequence-files/IGVFFI6226NROV/), [IGVFFI8589UWNL](/sequence-files/IGVFFI8589UWNL/), [IGVFFI7153UGVK](/sequence-files/IGVFFI7153UGVK/), [IGVFFI5062TFTZ](/sequence-files/IGVFFI5062TFTZ/), [IGVFFI4789BDNT](/sequence-files/IGVFFI4789BDNT/), [IGVFFI3605UGTT](/sequence-files/IGVFFI3605UGTT/), [IGVFFI3479SGDW](/sequence-files/IGVFFI3479SGDW/), [IGVFFI9133MIOX](/sequence-files/IGVFFI9133MIOX/), [IGVFFI0673DVOG](/sequence-files/IGVFFI0673DVOG/), [IGVFFI1499PCQB](/sequence-files/IGVFFI1499PCQB/), [IGVFFI6581YWEB](/sequence-files/IGVFFI6581YWEB/), [IGVFFI1350LNYJ](/sequence-files/IGVFFI1350LNYJ/), [IGVFFI0963OPXG](/sequence-files/IGVFFI0963OPXG/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS7100TFDB/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0839SQRJ](/measurement-sets/IGVFDS0839SQRJ/) 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": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS0839SQRJ/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS7100TFDB](/auxiliary-sets/IGVFDS7100TFDB/) has sequence file(s) [IGVFFI5357MXXH](/sequence-files/IGVFFI5357MXXH/), [IGVFFI6093YBAZ](/sequence-files/IGVFFI6093YBAZ/), [IGVFFI6611WMMZ](/sequence-files/IGVFFI6611WMMZ/), [IGVFFI5582FKUS](/sequence-files/IGVFFI5582FKUS/), [IGVFFI5683NIXR](/sequence-files/IGVFFI5683NIXR/), [IGVFFI0318GWBO](/sequence-files/IGVFFI0318GWBO/), [IGVFFI5176UXJE](/sequence-files/IGVFFI5176UXJE/), [IGVFFI3398EYGW](/sequence-files/IGVFFI3398EYGW/), [IGVFFI1028LFBE](/sequence-files/IGVFFI1028LFBE/), [IGVFFI4337UZYQ](/sequence-files/IGVFFI4337UZYQ/), [IGVFFI1594RLYS](/sequence-files/IGVFFI1594RLYS/), [IGVFFI2394UNNV](/sequence-files/IGVFFI2394UNNV/), [IGVFFI3311DACT](/sequence-files/IGVFFI3311DACT/), [IGVFFI4377YQQR](/sequence-files/IGVFFI4377YQQR/), [IGVFFI3739XFPS](/sequence-files/IGVFFI3739XFPS/), [IGVFFI4630DQJD](/sequence-files/IGVFFI4630DQJD/), [IGVFFI7130VZAO](/sequence-files/IGVFFI7130VZAO/), [IGVFFI4885ANSD](/sequence-files/IGVFFI4885ANSD/), [IGVFFI6370OHKN](/sequence-files/IGVFFI6370OHKN/), [IGVFFI2899LEMP](/sequence-files/IGVFFI2899LEMP/), [IGVFFI0501JGMG](/sequence-files/IGVFFI0501JGMG/), [IGVFFI4436PDOZ](/sequence-files/IGVFFI4436PDOZ/), [IGVFFI3562UGCX](/sequence-files/IGVFFI3562UGCX/), [IGVFFI3683VWLI](/sequence-files/IGVFFI3683VWLI/), [IGVFFI2613DCAO](/sequence-files/IGVFFI2613DCAO/), [IGVFFI0794PHCL](/sequence-files/IGVFFI0794PHCL/), [IGVFFI0242JSKB](/sequence-files/IGVFFI0242JSKB/), [IGVFFI3070RDZQ](/sequence-files/IGVFFI3070RDZQ/), [IGVFFI1118EWBM](/sequence-files/IGVFFI1118EWBM/), [IGVFFI8301AKCU](/sequence-files/IGVFFI8301AKCU/), [IGVFFI2441TLMB](/sequence-files/IGVFFI2441TLMB/), [IGVFFI8770XIYP](/sequence-files/IGVFFI8770XIYP/), [IGVFFI8601GRVM](/sequence-files/IGVFFI8601GRVM/), [IGVFFI7795QKJJ](/sequence-files/IGVFFI7795QKJJ/), [IGVFFI9740OJZC](/sequence-files/IGVFFI9740OJZC/), [IGVFFI6226NROV](/sequence-files/IGVFFI6226NROV/), [IGVFFI8589UWNL](/sequence-files/IGVFFI8589UWNL/), [IGVFFI7153UGVK](/sequence-files/IGVFFI7153UGVK/), [IGVFFI5062TFTZ](/sequence-files/IGVFFI5062TFTZ/), [IGVFFI4789BDNT](/sequence-files/IGVFFI4789BDNT/), [IGVFFI3605UGTT](/sequence-files/IGVFFI3605UGTT/), [IGVFFI3479SGDW](/sequence-files/IGVFFI3479SGDW/), [IGVFFI9133MIOX](/sequence-files/IGVFFI9133MIOX/), [IGVFFI0673DVOG](/sequence-files/IGVFFI0673DVOG/), [IGVFFI1499PCQB](/sequence-files/IGVFFI1499PCQB/), [IGVFFI6581YWEB](/sequence-files/IGVFFI6581YWEB/), [IGVFFI1350LNYJ](/sequence-files/IGVFFI1350LNYJ/), [IGVFFI0963OPXG](/sequence-files/IGVFFI0963OPXG/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 40,
"level_name": "WARNING",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS7100TFDB/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS7100TFDB](/auxiliary-sets/IGVFDS7100TFDB/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_file_set_for",
"path": "/auxiliary-sets/IGVFDS7100TFDB/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS7100TFDB/",
"accession": "IGVFDS7100TFDB",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep3-BinC_AmpliconSequencing_AuxiliarySet"
],
"file_set_type": "variant sequencing"
}
],
"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"
},
"control_file_sets": [
{
"@id": "/measurement-sets/IGVFDS5128CXIS/",
"accession": "IGVFDS5128CXIS",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-12-13T08:01:46.940716+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "experimental data",
"files": [],
"input_file_set_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.",
"preferred_assay_title": "Variant FlowFISH",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"release_timestamp": "2023-12-20T23:07:52.269795+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0890ULSF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0890ULSF",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep3-BinC"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2385DHZO/",
"accession": "IGVFDS2385DHZO",
"file_set_type": "guide library",
"summary": "Guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing"
}
],
"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": "THP-1 cell line, male, Homo sapiens (sorting details: FACS bin for 51-75% expression of PPIF) modified with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "21",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-13T09:07:24.652609+00:00",
"summary": "Variant FlowFISH integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"targeted_genes": [
{
"@id": "/genes/ENSG00000108179/",
"geneid": "ENSG00000108179",
"name": "peptidylprolyl isomerase F",
"symbol": "PPIF",
"synonyms": [
"rotamase F",
"CYP3",
"cyclophilin F",
"mitochondrial cyclophilin",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"CypD",
"Cyp-D",
"cyclophilin 3",
"cyclophilin D",
"CyP-M",
"peptidyl-prolyl cis-trans isomerase F, mitochondrial",
"PPIase F"
]
}
],
"uuid": "0aa9734d-678e-48de-9595-1ac94071e7db"
}