{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4715UUNW/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4715UUNW",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinB_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 measurement set [IGVFDS4715UUNW](/measurement-sets/IGVFDS4715UUNW/) has in progress subobject auxiliary set [IGVFDS0364VAST](/auxiliary-sets/IGVFDS0364VAST/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS4715UUNW/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM6465SGTZ](/in-vitro-systems/IGVFSM6465SGTZ/) 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/IGVFSM6465SGTZ/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4715UUNW](/measurement-sets/IGVFDS4715UUNW/) 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/IGVFDS4715UUNW/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS0364VAST](/auxiliary-sets/IGVFDS0364VAST/) has sequence file(s): [IGVFFI6377VEIZ](/sequence-files/IGVFFI6377VEIZ/), [IGVFFI7410FPKB](/sequence-files/IGVFFI7410FPKB/), [IGVFFI7140GDWU](/sequence-files/IGVFFI7140GDWU/), [IGVFFI2250LSBK](/sequence-files/IGVFFI2250LSBK/), [IGVFFI4103UDVM](/sequence-files/IGVFFI4103UDVM/), [IGVFFI5784GOVY](/sequence-files/IGVFFI5784GOVY/), [IGVFFI3144HJFC](/sequence-files/IGVFFI3144HJFC/), [IGVFFI4594INBA](/sequence-files/IGVFFI4594INBA/), [IGVFFI2689JYVN](/sequence-files/IGVFFI2689JYVN/), [IGVFFI9536XBVG](/sequence-files/IGVFFI9536XBVG/), [IGVFFI4356OTRP](/sequence-files/IGVFFI4356OTRP/), [IGVFFI9184CZBD](/sequence-files/IGVFFI9184CZBD/), [IGVFFI8420JRAJ](/sequence-files/IGVFFI8420JRAJ/), [IGVFFI7985PIGO](/sequence-files/IGVFFI7985PIGO/), [IGVFFI0823QNJP](/sequence-files/IGVFFI0823QNJP/), [IGVFFI8929XKOB](/sequence-files/IGVFFI8929XKOB/), [IGVFFI3110BEYO](/sequence-files/IGVFFI3110BEYO/), [IGVFFI1944OUXD](/sequence-files/IGVFFI1944OUXD/), [IGVFFI0274PUXE](/sequence-files/IGVFFI0274PUXE/), [IGVFFI3994GSTL](/sequence-files/IGVFFI3994GSTL/), [IGVFFI3607YKUC](/sequence-files/IGVFFI3607YKUC/), [IGVFFI2274SCHL](/sequence-files/IGVFFI2274SCHL/), [IGVFFI4955KZXD](/sequence-files/IGVFFI4955KZXD/), [IGVFFI5125IDOE](/sequence-files/IGVFFI5125IDOE/), [IGVFFI9229IWPT](/sequence-files/IGVFFI9229IWPT/), [IGVFFI6218NFQS](/sequence-files/IGVFFI6218NFQS/), [IGVFFI4610QDGV](/sequence-files/IGVFFI4610QDGV/), [IGVFFI7524IGSV](/sequence-files/IGVFFI7524IGSV/), [IGVFFI8617JKDI](/sequence-files/IGVFFI8617JKDI/), [IGVFFI7001JZLG](/sequence-files/IGVFFI7001JZLG/), [IGVFFI7284RNWP](/sequence-files/IGVFFI7284RNWP/), [IGVFFI6880IFRV](/sequence-files/IGVFFI6880IFRV/), [IGVFFI4708VMRK](/sequence-files/IGVFFI4708VMRK/), [IGVFFI5242IPQS](/sequence-files/IGVFFI5242IPQS/), [IGVFFI0412PDLA](/sequence-files/IGVFFI0412PDLA/), [IGVFFI7552QIXL](/sequence-files/IGVFFI7552QIXL/), [IGVFFI2130ELMO](/sequence-files/IGVFFI2130ELMO/), [IGVFFI2937NHTG](/sequence-files/IGVFFI2937NHTG/), [IGVFFI9325JLRR](/sequence-files/IGVFFI9325JLRR/), [IGVFFI2160VMLA](/sequence-files/IGVFFI2160VMLA/), [IGVFFI2926TOQM](/sequence-files/IGVFFI2926TOQM/), [IGVFFI6251VYGU](/sequence-files/IGVFFI6251VYGU/), [IGVFFI2327HPPA](/sequence-files/IGVFFI2327HPPA/), [IGVFFI5611IJQX](/sequence-files/IGVFFI5611IJQX/), [IGVFFI9973MEOU](/sequence-files/IGVFFI9973MEOU/), [IGVFFI0914AOQT](/sequence-files/IGVFFI0914AOQT/), [IGVFFI9772SKUX](/sequence-files/IGVFFI9772SKUX/), [IGVFFI1499WAPM](/sequence-files/IGVFFI1499WAPM/) 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/IGVFDS0364VAST/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS0364VAST](/auxiliary-sets/IGVFDS0364VAST/) has sequence file(s) [IGVFFI6377VEIZ](/sequence-files/IGVFFI6377VEIZ/), [IGVFFI7410FPKB](/sequence-files/IGVFFI7410FPKB/), [IGVFFI7140GDWU](/sequence-files/IGVFFI7140GDWU/), [IGVFFI2250LSBK](/sequence-files/IGVFFI2250LSBK/), [IGVFFI4103UDVM](/sequence-files/IGVFFI4103UDVM/), [IGVFFI5784GOVY](/sequence-files/IGVFFI5784GOVY/), [IGVFFI3144HJFC](/sequence-files/IGVFFI3144HJFC/), [IGVFFI4594INBA](/sequence-files/IGVFFI4594INBA/), [IGVFFI2689JYVN](/sequence-files/IGVFFI2689JYVN/), [IGVFFI9536XBVG](/sequence-files/IGVFFI9536XBVG/), [IGVFFI4356OTRP](/sequence-files/IGVFFI4356OTRP/), [IGVFFI9184CZBD](/sequence-files/IGVFFI9184CZBD/), [IGVFFI8420JRAJ](/sequence-files/IGVFFI8420JRAJ/), [IGVFFI7985PIGO](/sequence-files/IGVFFI7985PIGO/), [IGVFFI0823QNJP](/sequence-files/IGVFFI0823QNJP/), [IGVFFI8929XKOB](/sequence-files/IGVFFI8929XKOB/), [IGVFFI3110BEYO](/sequence-files/IGVFFI3110BEYO/), [IGVFFI1944OUXD](/sequence-files/IGVFFI1944OUXD/), [IGVFFI0274PUXE](/sequence-files/IGVFFI0274PUXE/), [IGVFFI3994GSTL](/sequence-files/IGVFFI3994GSTL/), [IGVFFI3607YKUC](/sequence-files/IGVFFI3607YKUC/), [IGVFFI2274SCHL](/sequence-files/IGVFFI2274SCHL/), [IGVFFI4955KZXD](/sequence-files/IGVFFI4955KZXD/), [IGVFFI5125IDOE](/sequence-files/IGVFFI5125IDOE/), [IGVFFI9229IWPT](/sequence-files/IGVFFI9229IWPT/), [IGVFFI6218NFQS](/sequence-files/IGVFFI6218NFQS/), [IGVFFI4610QDGV](/sequence-files/IGVFFI4610QDGV/), [IGVFFI7524IGSV](/sequence-files/IGVFFI7524IGSV/), [IGVFFI8617JKDI](/sequence-files/IGVFFI8617JKDI/), [IGVFFI7001JZLG](/sequence-files/IGVFFI7001JZLG/), [IGVFFI7284RNWP](/sequence-files/IGVFFI7284RNWP/), [IGVFFI6880IFRV](/sequence-files/IGVFFI6880IFRV/), [IGVFFI4708VMRK](/sequence-files/IGVFFI4708VMRK/), [IGVFFI5242IPQS](/sequence-files/IGVFFI5242IPQS/), [IGVFFI0412PDLA](/sequence-files/IGVFFI0412PDLA/), [IGVFFI7552QIXL](/sequence-files/IGVFFI7552QIXL/), [IGVFFI2130ELMO](/sequence-files/IGVFFI2130ELMO/), [IGVFFI2937NHTG](/sequence-files/IGVFFI2937NHTG/), [IGVFFI9325JLRR](/sequence-files/IGVFFI9325JLRR/), [IGVFFI2160VMLA](/sequence-files/IGVFFI2160VMLA/), [IGVFFI2926TOQM](/sequence-files/IGVFFI2926TOQM/), [IGVFFI6251VYGU](/sequence-files/IGVFFI6251VYGU/), [IGVFFI2327HPPA](/sequence-files/IGVFFI2327HPPA/), [IGVFFI5611IJQX](/sequence-files/IGVFFI5611IJQX/), [IGVFFI9973MEOU](/sequence-files/IGVFFI9973MEOU/), [IGVFFI0914AOQT](/sequence-files/IGVFFI0914AOQT/), [IGVFFI9772SKUX](/sequence-files/IGVFFI9772SKUX/), [IGVFFI1499WAPM](/sequence-files/IGVFFI1499WAPM/) 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/IGVFDS0364VAST/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS0364VAST](/auxiliary-sets/IGVFDS0364VAST/) 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/IGVFDS0364VAST/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0364VAST/",
"accession": "IGVFDS0364VAST",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinB_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/IGVFDS5864UGFT/",
"accession": "IGVFDS5864UGFT",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:50:10.832992+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/IGVFDS3423PSID/"
],
"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": "2023-12-20T23:06:19.064235+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6465SGTZ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6465SGTZ",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinB"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6982DESN/",
"accession": "IGVFDS6982DESN",
"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 26-50% 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": "2023-12-05T23:04:43.469258+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": "c347f985-d209-45b2-9862-928f792992b9"
}