{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3765SWWC/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3765SWWC",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep4-BinA_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 [IGVFSM2557IAGR](/in-vitro-systems/IGVFSM2557IAGR/) 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/IGVFSM2557IAGR/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS3765SWWC](/measurement-sets/IGVFDS3765SWWC/) has in progress subobject auxiliary set [IGVFDS8419EQUX](/auxiliary-sets/IGVFDS8419EQUX/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS3765SWWC/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS3765SWWC](/measurement-sets/IGVFDS3765SWWC/) 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/IGVFDS3765SWWC/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8419EQUX](/auxiliary-sets/IGVFDS8419EQUX/) has sequence file(s): [IGVFFI8980OZIR](/sequence-files/IGVFFI8980OZIR/), [IGVFFI1426JKWP](/sequence-files/IGVFFI1426JKWP/), [IGVFFI4139XIUZ](/sequence-files/IGVFFI4139XIUZ/), [IGVFFI0760ZZUA](/sequence-files/IGVFFI0760ZZUA/), [IGVFFI6728VMSV](/sequence-files/IGVFFI6728VMSV/), [IGVFFI3902DBNN](/sequence-files/IGVFFI3902DBNN/), [IGVFFI3155EKEY](/sequence-files/IGVFFI3155EKEY/), [IGVFFI4271CIHQ](/sequence-files/IGVFFI4271CIHQ/), [IGVFFI6987FQET](/sequence-files/IGVFFI6987FQET/), [IGVFFI8651DLZB](/sequence-files/IGVFFI8651DLZB/), [IGVFFI9051TCCZ](/sequence-files/IGVFFI9051TCCZ/), [IGVFFI1800NRAG](/sequence-files/IGVFFI1800NRAG/), [IGVFFI2510ASDE](/sequence-files/IGVFFI2510ASDE/), [IGVFFI7027GQXC](/sequence-files/IGVFFI7027GQXC/), [IGVFFI7476FAEF](/sequence-files/IGVFFI7476FAEF/), [IGVFFI1424IKFY](/sequence-files/IGVFFI1424IKFY/), [IGVFFI9366IRCH](/sequence-files/IGVFFI9366IRCH/), [IGVFFI8994SLCX](/sequence-files/IGVFFI8994SLCX/), [IGVFFI0601XPFY](/sequence-files/IGVFFI0601XPFY/), [IGVFFI5177VTTC](/sequence-files/IGVFFI5177VTTC/), [IGVFFI2813ARMS](/sequence-files/IGVFFI2813ARMS/), [IGVFFI7239FHHM](/sequence-files/IGVFFI7239FHHM/), [IGVFFI3161DWEU](/sequence-files/IGVFFI3161DWEU/), [IGVFFI4563ZWDG](/sequence-files/IGVFFI4563ZWDG/), [IGVFFI5420GUHQ](/sequence-files/IGVFFI5420GUHQ/), [IGVFFI8170ELEN](/sequence-files/IGVFFI8170ELEN/), [IGVFFI4925QRTR](/sequence-files/IGVFFI4925QRTR/), [IGVFFI8435LCYS](/sequence-files/IGVFFI8435LCYS/), [IGVFFI2673CTYV](/sequence-files/IGVFFI2673CTYV/), [IGVFFI5845SYKV](/sequence-files/IGVFFI5845SYKV/), [IGVFFI0617MYPV](/sequence-files/IGVFFI0617MYPV/), [IGVFFI7392SJRB](/sequence-files/IGVFFI7392SJRB/), [IGVFFI1667VREQ](/sequence-files/IGVFFI1667VREQ/), [IGVFFI6151SNGD](/sequence-files/IGVFFI6151SNGD/), [IGVFFI6249UMFI](/sequence-files/IGVFFI6249UMFI/), [IGVFFI5710TBVP](/sequence-files/IGVFFI5710TBVP/), [IGVFFI6268SEMT](/sequence-files/IGVFFI6268SEMT/), [IGVFFI5496HCDH](/sequence-files/IGVFFI5496HCDH/), [IGVFFI4537FCCI](/sequence-files/IGVFFI4537FCCI/), [IGVFFI8363TESH](/sequence-files/IGVFFI8363TESH/), [IGVFFI6865FKIY](/sequence-files/IGVFFI6865FKIY/), [IGVFFI4650NLWV](/sequence-files/IGVFFI4650NLWV/), [IGVFFI7807MTEI](/sequence-files/IGVFFI7807MTEI/), [IGVFFI3826WHUR](/sequence-files/IGVFFI3826WHUR/), [IGVFFI3587LMNL](/sequence-files/IGVFFI3587LMNL/), [IGVFFI8671NHNC](/sequence-files/IGVFFI8671NHNC/), [IGVFFI1585IGGH](/sequence-files/IGVFFI1585IGGH/) 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/IGVFDS8419EQUX/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8419EQUX](/auxiliary-sets/IGVFDS8419EQUX/) has sequence file(s) [IGVFFI8980OZIR](/sequence-files/IGVFFI8980OZIR/), [IGVFFI1426JKWP](/sequence-files/IGVFFI1426JKWP/), [IGVFFI4139XIUZ](/sequence-files/IGVFFI4139XIUZ/), [IGVFFI0760ZZUA](/sequence-files/IGVFFI0760ZZUA/), [IGVFFI6728VMSV](/sequence-files/IGVFFI6728VMSV/), [IGVFFI3902DBNN](/sequence-files/IGVFFI3902DBNN/), [IGVFFI3155EKEY](/sequence-files/IGVFFI3155EKEY/), [IGVFFI4271CIHQ](/sequence-files/IGVFFI4271CIHQ/), [IGVFFI6987FQET](/sequence-files/IGVFFI6987FQET/), [IGVFFI8651DLZB](/sequence-files/IGVFFI8651DLZB/), [IGVFFI9051TCCZ](/sequence-files/IGVFFI9051TCCZ/), [IGVFFI1800NRAG](/sequence-files/IGVFFI1800NRAG/), [IGVFFI2510ASDE](/sequence-files/IGVFFI2510ASDE/), [IGVFFI7027GQXC](/sequence-files/IGVFFI7027GQXC/), [IGVFFI7476FAEF](/sequence-files/IGVFFI7476FAEF/), [IGVFFI1424IKFY](/sequence-files/IGVFFI1424IKFY/), [IGVFFI9366IRCH](/sequence-files/IGVFFI9366IRCH/), [IGVFFI8994SLCX](/sequence-files/IGVFFI8994SLCX/), [IGVFFI0601XPFY](/sequence-files/IGVFFI0601XPFY/), [IGVFFI5177VTTC](/sequence-files/IGVFFI5177VTTC/), [IGVFFI2813ARMS](/sequence-files/IGVFFI2813ARMS/), [IGVFFI7239FHHM](/sequence-files/IGVFFI7239FHHM/), [IGVFFI3161DWEU](/sequence-files/IGVFFI3161DWEU/), [IGVFFI4563ZWDG](/sequence-files/IGVFFI4563ZWDG/), [IGVFFI5420GUHQ](/sequence-files/IGVFFI5420GUHQ/), [IGVFFI8170ELEN](/sequence-files/IGVFFI8170ELEN/), [IGVFFI4925QRTR](/sequence-files/IGVFFI4925QRTR/), [IGVFFI8435LCYS](/sequence-files/IGVFFI8435LCYS/), [IGVFFI2673CTYV](/sequence-files/IGVFFI2673CTYV/), [IGVFFI5845SYKV](/sequence-files/IGVFFI5845SYKV/), [IGVFFI0617MYPV](/sequence-files/IGVFFI0617MYPV/), [IGVFFI7392SJRB](/sequence-files/IGVFFI7392SJRB/), [IGVFFI1667VREQ](/sequence-files/IGVFFI1667VREQ/), [IGVFFI6151SNGD](/sequence-files/IGVFFI6151SNGD/), [IGVFFI6249UMFI](/sequence-files/IGVFFI6249UMFI/), [IGVFFI5710TBVP](/sequence-files/IGVFFI5710TBVP/), [IGVFFI6268SEMT](/sequence-files/IGVFFI6268SEMT/), [IGVFFI5496HCDH](/sequence-files/IGVFFI5496HCDH/), [IGVFFI4537FCCI](/sequence-files/IGVFFI4537FCCI/), [IGVFFI8363TESH](/sequence-files/IGVFFI8363TESH/), [IGVFFI6865FKIY](/sequence-files/IGVFFI6865FKIY/), [IGVFFI4650NLWV](/sequence-files/IGVFFI4650NLWV/), [IGVFFI7807MTEI](/sequence-files/IGVFFI7807MTEI/), [IGVFFI3826WHUR](/sequence-files/IGVFFI3826WHUR/), [IGVFFI3587LMNL](/sequence-files/IGVFFI3587LMNL/), [IGVFFI8671NHNC](/sequence-files/IGVFFI8671NHNC/), [IGVFFI1585IGGH](/sequence-files/IGVFFI1585IGGH/) 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/IGVFDS8419EQUX/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS8419EQUX](/auxiliary-sets/IGVFDS8419EQUX/) 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/IGVFDS8419EQUX/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8419EQUX/",
"accession": "IGVFDS8419EQUX",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep4-BinA_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": "2023-12-13T08:01:47.842444+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": "2023-12-20T23:07:19.788125+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2557IAGR/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2557IAGR",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep4-BinA"
],
"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 0-25% 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": "2023-12-13T09:15:30.255398+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": "e950d39b-28cd-4837-bea2-add0e6ce5e5c"
}