{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5601DSMT/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5601DSMT",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-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 in vitro system [IGVFSM1683OFWB](/in-vitro-systems/IGVFSM1683OFWB/) has in progress subobject construct library set [IGVFDS2374NXLW](/construct-library-sets/IGVFDS2374NXLW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM1683OFWB/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS5601DSMT](/measurement-sets/IGVFDS5601DSMT/) has in progress subobject auxiliary set [IGVFDS0823ECNW](/auxiliary-sets/IGVFDS0823ECNW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS5601DSMT/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS0823ECNW](/auxiliary-sets/IGVFDS0823ECNW/) has sequence file(s): [IGVFFI4864DDOF](/sequence-files/IGVFFI4864DDOF/), [IGVFFI5089YLYB](/sequence-files/IGVFFI5089YLYB/), [IGVFFI3915EGRV](/sequence-files/IGVFFI3915EGRV/), [IGVFFI8756VSTR](/sequence-files/IGVFFI8756VSTR/), [IGVFFI4936XVSR](/sequence-files/IGVFFI4936XVSR/), [IGVFFI7444OBIU](/sequence-files/IGVFFI7444OBIU/), [IGVFFI4676IJRY](/sequence-files/IGVFFI4676IJRY/), [IGVFFI7360DGNO](/sequence-files/IGVFFI7360DGNO/), [IGVFFI8460TPOZ](/sequence-files/IGVFFI8460TPOZ/), [IGVFFI1362FVKL](/sequence-files/IGVFFI1362FVKL/), [IGVFFI3813XVHV](/sequence-files/IGVFFI3813XVHV/), [IGVFFI5441ERNT](/sequence-files/IGVFFI5441ERNT/), [IGVFFI4783IWIC](/sequence-files/IGVFFI4783IWIC/), [IGVFFI2662EXCE](/sequence-files/IGVFFI2662EXCE/), [IGVFFI1523DBUY](/sequence-files/IGVFFI1523DBUY/), [IGVFFI7369CIKM](/sequence-files/IGVFFI7369CIKM/), [IGVFFI1307TQSQ](/sequence-files/IGVFFI1307TQSQ/), [IGVFFI6246XNYB](/sequence-files/IGVFFI6246XNYB/), [IGVFFI5757EIZU](/sequence-files/IGVFFI5757EIZU/), [IGVFFI1309QTQZ](/sequence-files/IGVFFI1309QTQZ/), [IGVFFI4955YDRG](/sequence-files/IGVFFI4955YDRG/), [IGVFFI3515MQKE](/sequence-files/IGVFFI3515MQKE/), [IGVFFI3869CPGH](/sequence-files/IGVFFI3869CPGH/), [IGVFFI3131OJGE](/sequence-files/IGVFFI3131OJGE/), [IGVFFI4019NMPR](/sequence-files/IGVFFI4019NMPR/), [IGVFFI1930YUHE](/sequence-files/IGVFFI1930YUHE/), [IGVFFI1864UYET](/sequence-files/IGVFFI1864UYET/), [IGVFFI9642LJDO](/sequence-files/IGVFFI9642LJDO/), [IGVFFI2824YXTH](/sequence-files/IGVFFI2824YXTH/), [IGVFFI4131ZXYF](/sequence-files/IGVFFI4131ZXYF/), [IGVFFI8751QQNX](/sequence-files/IGVFFI8751QQNX/), [IGVFFI7374RRXR](/sequence-files/IGVFFI7374RRXR/), [IGVFFI1546PTDD](/sequence-files/IGVFFI1546PTDD/), [IGVFFI6218HRIS](/sequence-files/IGVFFI6218HRIS/), [IGVFFI3742WOXP](/sequence-files/IGVFFI3742WOXP/), [IGVFFI3387PYFS](/sequence-files/IGVFFI3387PYFS/), [IGVFFI8055KEXV](/sequence-files/IGVFFI8055KEXV/), [IGVFFI2679IQIT](/sequence-files/IGVFFI2679IQIT/), [IGVFFI4424XQZK](/sequence-files/IGVFFI4424XQZK/), [IGVFFI6437PYCR](/sequence-files/IGVFFI6437PYCR/), [IGVFFI6842UARR](/sequence-files/IGVFFI6842UARR/), [IGVFFI2137UJYR](/sequence-files/IGVFFI2137UJYR/), [IGVFFI2610OUCN](/sequence-files/IGVFFI2610OUCN/), [IGVFFI9804ZJBX](/sequence-files/IGVFFI9804ZJBX/), [IGVFFI3175MPTK](/sequence-files/IGVFFI3175MPTK/), [IGVFFI2074DZDG](/sequence-files/IGVFFI2074DZDG/), [IGVFFI2133OIWQ](/sequence-files/IGVFFI2133OIWQ/), [IGVFFI6875GFJZ](/sequence-files/IGVFFI6875GFJZ/) 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/IGVFDS0823ECNW/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5601DSMT](/measurement-sets/IGVFDS5601DSMT/) 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/IGVFDS5601DSMT/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS0823ECNW](/auxiliary-sets/IGVFDS0823ECNW/) has sequence file(s) [IGVFFI4864DDOF](/sequence-files/IGVFFI4864DDOF/), [IGVFFI5089YLYB](/sequence-files/IGVFFI5089YLYB/), [IGVFFI3915EGRV](/sequence-files/IGVFFI3915EGRV/), [IGVFFI8756VSTR](/sequence-files/IGVFFI8756VSTR/), [IGVFFI4936XVSR](/sequence-files/IGVFFI4936XVSR/), [IGVFFI7444OBIU](/sequence-files/IGVFFI7444OBIU/), [IGVFFI4676IJRY](/sequence-files/IGVFFI4676IJRY/), [IGVFFI7360DGNO](/sequence-files/IGVFFI7360DGNO/), [IGVFFI8460TPOZ](/sequence-files/IGVFFI8460TPOZ/), [IGVFFI1362FVKL](/sequence-files/IGVFFI1362FVKL/), [IGVFFI3813XVHV](/sequence-files/IGVFFI3813XVHV/), [IGVFFI5441ERNT](/sequence-files/IGVFFI5441ERNT/), [IGVFFI4783IWIC](/sequence-files/IGVFFI4783IWIC/), [IGVFFI2662EXCE](/sequence-files/IGVFFI2662EXCE/), [IGVFFI1523DBUY](/sequence-files/IGVFFI1523DBUY/), [IGVFFI7369CIKM](/sequence-files/IGVFFI7369CIKM/), [IGVFFI1307TQSQ](/sequence-files/IGVFFI1307TQSQ/), [IGVFFI6246XNYB](/sequence-files/IGVFFI6246XNYB/), [IGVFFI5757EIZU](/sequence-files/IGVFFI5757EIZU/), [IGVFFI1309QTQZ](/sequence-files/IGVFFI1309QTQZ/), [IGVFFI4955YDRG](/sequence-files/IGVFFI4955YDRG/), [IGVFFI3515MQKE](/sequence-files/IGVFFI3515MQKE/), [IGVFFI3869CPGH](/sequence-files/IGVFFI3869CPGH/), [IGVFFI3131OJGE](/sequence-files/IGVFFI3131OJGE/), [IGVFFI4019NMPR](/sequence-files/IGVFFI4019NMPR/), [IGVFFI1930YUHE](/sequence-files/IGVFFI1930YUHE/), [IGVFFI1864UYET](/sequence-files/IGVFFI1864UYET/), [IGVFFI9642LJDO](/sequence-files/IGVFFI9642LJDO/), [IGVFFI2824YXTH](/sequence-files/IGVFFI2824YXTH/), [IGVFFI4131ZXYF](/sequence-files/IGVFFI4131ZXYF/), [IGVFFI8751QQNX](/sequence-files/IGVFFI8751QQNX/), [IGVFFI7374RRXR](/sequence-files/IGVFFI7374RRXR/), [IGVFFI1546PTDD](/sequence-files/IGVFFI1546PTDD/), [IGVFFI6218HRIS](/sequence-files/IGVFFI6218HRIS/), [IGVFFI3742WOXP](/sequence-files/IGVFFI3742WOXP/), [IGVFFI3387PYFS](/sequence-files/IGVFFI3387PYFS/), [IGVFFI8055KEXV](/sequence-files/IGVFFI8055KEXV/), [IGVFFI2679IQIT](/sequence-files/IGVFFI2679IQIT/), [IGVFFI4424XQZK](/sequence-files/IGVFFI4424XQZK/), [IGVFFI6437PYCR](/sequence-files/IGVFFI6437PYCR/), [IGVFFI6842UARR](/sequence-files/IGVFFI6842UARR/), [IGVFFI2137UJYR](/sequence-files/IGVFFI2137UJYR/), [IGVFFI2610OUCN](/sequence-files/IGVFFI2610OUCN/), [IGVFFI9804ZJBX](/sequence-files/IGVFFI9804ZJBX/), [IGVFFI3175MPTK](/sequence-files/IGVFFI3175MPTK/), [IGVFFI2074DZDG](/sequence-files/IGVFFI2074DZDG/), [IGVFFI2133OIWQ](/sequence-files/IGVFFI2133OIWQ/), [IGVFFI6875GFJZ](/sequence-files/IGVFFI6875GFJZ/) 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/IGVFDS0823ECNW/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS0823ECNW](/auxiliary-sets/IGVFDS0823ECNW/) 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/IGVFDS0823ECNW/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0823ECNW/",
"accession": "IGVFDS0823ECNW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-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/IGVFDS4989HPTW/",
"accession": "IGVFDS4989HPTW",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:49:15.417382+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/IGVFDS5031MNRR/"
],
"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": "2023-12-20T23:05:28.817263+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1683OFWB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1683OFWB",
"aliases": [
"jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinB"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2374NXLW/",
"accession": "IGVFDS2374NXLW",
"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": "20",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T22:29:43.102677+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": "fd6e5d84-173b-4f03-8de0-67bbec8d433f"
}