{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5338RAZZ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5338RAZZ",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-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 [IGVFSM3864UXYU](/in-vitro-systems/IGVFSM3864UXYU/) 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/IGVFSM3864UXYU/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS5338RAZZ](/measurement-sets/IGVFDS5338RAZZ/) has in progress subobject auxiliary set [IGVFDS7255CZPZ](/auxiliary-sets/IGVFDS7255CZPZ/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS5338RAZZ/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS7255CZPZ](/auxiliary-sets/IGVFDS7255CZPZ/) has sequence file(s): [IGVFFI8123RRRX](/sequence-files/IGVFFI8123RRRX/), [IGVFFI7918PGFC](/sequence-files/IGVFFI7918PGFC/), [IGVFFI2930FLLT](/sequence-files/IGVFFI2930FLLT/), [IGVFFI8716XXBJ](/sequence-files/IGVFFI8716XXBJ/), [IGVFFI4645WNTT](/sequence-files/IGVFFI4645WNTT/), [IGVFFI3528DWKZ](/sequence-files/IGVFFI3528DWKZ/), [IGVFFI8347EAYK](/sequence-files/IGVFFI8347EAYK/), [IGVFFI6922JODM](/sequence-files/IGVFFI6922JODM/), [IGVFFI1523OVVN](/sequence-files/IGVFFI1523OVVN/), [IGVFFI7809ROCB](/sequence-files/IGVFFI7809ROCB/), [IGVFFI8323KPRD](/sequence-files/IGVFFI8323KPRD/), [IGVFFI7436KQOD](/sequence-files/IGVFFI7436KQOD/), [IGVFFI8171RHQG](/sequence-files/IGVFFI8171RHQG/), [IGVFFI7161PJBN](/sequence-files/IGVFFI7161PJBN/), [IGVFFI3984LMGQ](/sequence-files/IGVFFI3984LMGQ/), [IGVFFI7068JEKU](/sequence-files/IGVFFI7068JEKU/), [IGVFFI2430CSIN](/sequence-files/IGVFFI2430CSIN/), [IGVFFI7699CGJJ](/sequence-files/IGVFFI7699CGJJ/), [IGVFFI3064SFSF](/sequence-files/IGVFFI3064SFSF/), [IGVFFI3692HBQW](/sequence-files/IGVFFI3692HBQW/), [IGVFFI4467AGCN](/sequence-files/IGVFFI4467AGCN/), [IGVFFI7562QQOH](/sequence-files/IGVFFI7562QQOH/), [IGVFFI0578YVYP](/sequence-files/IGVFFI0578YVYP/), [IGVFFI1113PWJO](/sequence-files/IGVFFI1113PWJO/), [IGVFFI8927CNBV](/sequence-files/IGVFFI8927CNBV/), [IGVFFI6373RZHU](/sequence-files/IGVFFI6373RZHU/), [IGVFFI9224HUFZ](/sequence-files/IGVFFI9224HUFZ/), [IGVFFI3408TFGI](/sequence-files/IGVFFI3408TFGI/), [IGVFFI3326ZKID](/sequence-files/IGVFFI3326ZKID/), [IGVFFI8150HSEV](/sequence-files/IGVFFI8150HSEV/), [IGVFFI4089MBBT](/sequence-files/IGVFFI4089MBBT/), [IGVFFI7577AYTS](/sequence-files/IGVFFI7577AYTS/), [IGVFFI6569DBKO](/sequence-files/IGVFFI6569DBKO/), [IGVFFI9640UJQB](/sequence-files/IGVFFI9640UJQB/), [IGVFFI6096RFED](/sequence-files/IGVFFI6096RFED/), [IGVFFI5021OMEF](/sequence-files/IGVFFI5021OMEF/), [IGVFFI0362PXLI](/sequence-files/IGVFFI0362PXLI/), [IGVFFI7821JUZT](/sequence-files/IGVFFI7821JUZT/), [IGVFFI3975HQQX](/sequence-files/IGVFFI3975HQQX/), [IGVFFI6547ANUD](/sequence-files/IGVFFI6547ANUD/), [IGVFFI0010HKZD](/sequence-files/IGVFFI0010HKZD/), [IGVFFI5439NCZM](/sequence-files/IGVFFI5439NCZM/), [IGVFFI0210YMGF](/sequence-files/IGVFFI0210YMGF/), [IGVFFI9025KSGO](/sequence-files/IGVFFI9025KSGO/), [IGVFFI8638ZZWB](/sequence-files/IGVFFI8638ZZWB/), [IGVFFI0926MSUN](/sequence-files/IGVFFI0926MSUN/), [IGVFFI7459HGYL](/sequence-files/IGVFFI7459HGYL/), [IGVFFI2744GMUW](/sequence-files/IGVFFI2744GMUW/) 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/IGVFDS7255CZPZ/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5338RAZZ](/measurement-sets/IGVFDS5338RAZZ/) 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/IGVFDS5338RAZZ/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS7255CZPZ](/auxiliary-sets/IGVFDS7255CZPZ/) has sequence file(s) [IGVFFI8123RRRX](/sequence-files/IGVFFI8123RRRX/), [IGVFFI7918PGFC](/sequence-files/IGVFFI7918PGFC/), [IGVFFI2930FLLT](/sequence-files/IGVFFI2930FLLT/), [IGVFFI8716XXBJ](/sequence-files/IGVFFI8716XXBJ/), [IGVFFI4645WNTT](/sequence-files/IGVFFI4645WNTT/), [IGVFFI3528DWKZ](/sequence-files/IGVFFI3528DWKZ/), [IGVFFI8347EAYK](/sequence-files/IGVFFI8347EAYK/), [IGVFFI6922JODM](/sequence-files/IGVFFI6922JODM/), [IGVFFI1523OVVN](/sequence-files/IGVFFI1523OVVN/), [IGVFFI7809ROCB](/sequence-files/IGVFFI7809ROCB/), [IGVFFI8323KPRD](/sequence-files/IGVFFI8323KPRD/), [IGVFFI7436KQOD](/sequence-files/IGVFFI7436KQOD/), [IGVFFI8171RHQG](/sequence-files/IGVFFI8171RHQG/), [IGVFFI7161PJBN](/sequence-files/IGVFFI7161PJBN/), [IGVFFI3984LMGQ](/sequence-files/IGVFFI3984LMGQ/), [IGVFFI7068JEKU](/sequence-files/IGVFFI7068JEKU/), [IGVFFI2430CSIN](/sequence-files/IGVFFI2430CSIN/), [IGVFFI7699CGJJ](/sequence-files/IGVFFI7699CGJJ/), [IGVFFI3064SFSF](/sequence-files/IGVFFI3064SFSF/), [IGVFFI3692HBQW](/sequence-files/IGVFFI3692HBQW/), [IGVFFI4467AGCN](/sequence-files/IGVFFI4467AGCN/), [IGVFFI7562QQOH](/sequence-files/IGVFFI7562QQOH/), [IGVFFI0578YVYP](/sequence-files/IGVFFI0578YVYP/), [IGVFFI1113PWJO](/sequence-files/IGVFFI1113PWJO/), [IGVFFI8927CNBV](/sequence-files/IGVFFI8927CNBV/), [IGVFFI6373RZHU](/sequence-files/IGVFFI6373RZHU/), [IGVFFI9224HUFZ](/sequence-files/IGVFFI9224HUFZ/), [IGVFFI3408TFGI](/sequence-files/IGVFFI3408TFGI/), [IGVFFI3326ZKID](/sequence-files/IGVFFI3326ZKID/), [IGVFFI8150HSEV](/sequence-files/IGVFFI8150HSEV/), [IGVFFI4089MBBT](/sequence-files/IGVFFI4089MBBT/), [IGVFFI7577AYTS](/sequence-files/IGVFFI7577AYTS/), [IGVFFI6569DBKO](/sequence-files/IGVFFI6569DBKO/), [IGVFFI9640UJQB](/sequence-files/IGVFFI9640UJQB/), [IGVFFI6096RFED](/sequence-files/IGVFFI6096RFED/), [IGVFFI5021OMEF](/sequence-files/IGVFFI5021OMEF/), [IGVFFI0362PXLI](/sequence-files/IGVFFI0362PXLI/), [IGVFFI7821JUZT](/sequence-files/IGVFFI7821JUZT/), [IGVFFI3975HQQX](/sequence-files/IGVFFI3975HQQX/), [IGVFFI6547ANUD](/sequence-files/IGVFFI6547ANUD/), [IGVFFI0010HKZD](/sequence-files/IGVFFI0010HKZD/), [IGVFFI5439NCZM](/sequence-files/IGVFFI5439NCZM/), [IGVFFI0210YMGF](/sequence-files/IGVFFI0210YMGF/), [IGVFFI9025KSGO](/sequence-files/IGVFFI9025KSGO/), [IGVFFI8638ZZWB](/sequence-files/IGVFFI8638ZZWB/), [IGVFFI0926MSUN](/sequence-files/IGVFFI0926MSUN/), [IGVFFI7459HGYL](/sequence-files/IGVFFI7459HGYL/), [IGVFFI2744GMUW](/sequence-files/IGVFFI2744GMUW/) 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/IGVFDS7255CZPZ/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS7255CZPZ](/auxiliary-sets/IGVFDS7255CZPZ/) 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/IGVFDS7255CZPZ/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS7255CZPZ/",
"accession": "IGVFDS7255CZPZ",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-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": "2023-12-13T08:01:43.885618+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": "2023-12-20T23:07:59.549983+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3864UXYU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3864UXYU",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-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": "2023-12-13T08:50:39.721958+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": "cfcf5597-a68e-4cce-969c-5e1581dd786e"
}