{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2940LDCT/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2940LDCT",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-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 [IGVFSM3122QCVP](/in-vitro-systems/IGVFSM3122QCVP/) 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/IGVFSM3122QCVP/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS2940LDCT](/measurement-sets/IGVFDS2940LDCT/) has in progress subobject auxiliary set [IGVFDS4920QDPH](/auxiliary-sets/IGVFDS4920QDPH/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS2940LDCT/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2940LDCT](/measurement-sets/IGVFDS2940LDCT/) 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/IGVFDS2940LDCT/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS4920QDPH](/auxiliary-sets/IGVFDS4920QDPH/) has sequence file(s): [IGVFFI0689DCGL](/sequence-files/IGVFFI0689DCGL/), [IGVFFI3663MZAM](/sequence-files/IGVFFI3663MZAM/), [IGVFFI8824DFMJ](/sequence-files/IGVFFI8824DFMJ/), [IGVFFI3454DKAF](/sequence-files/IGVFFI3454DKAF/), [IGVFFI8240MXWF](/sequence-files/IGVFFI8240MXWF/), [IGVFFI3159FCSV](/sequence-files/IGVFFI3159FCSV/), [IGVFFI8073MEFZ](/sequence-files/IGVFFI8073MEFZ/), [IGVFFI8158ZOSQ](/sequence-files/IGVFFI8158ZOSQ/), [IGVFFI3429UOCE](/sequence-files/IGVFFI3429UOCE/), [IGVFFI8054NIXV](/sequence-files/IGVFFI8054NIXV/), [IGVFFI4228DTGP](/sequence-files/IGVFFI4228DTGP/), [IGVFFI8776UIEY](/sequence-files/IGVFFI8776UIEY/), [IGVFFI5231YNFI](/sequence-files/IGVFFI5231YNFI/), [IGVFFI6995XLQZ](/sequence-files/IGVFFI6995XLQZ/), [IGVFFI8826ESGW](/sequence-files/IGVFFI8826ESGW/), [IGVFFI5410XGYG](/sequence-files/IGVFFI5410XGYG/), [IGVFFI7367RFXB](/sequence-files/IGVFFI7367RFXB/), [IGVFFI2720ZSWR](/sequence-files/IGVFFI2720ZSWR/), [IGVFFI5610OGTO](/sequence-files/IGVFFI5610OGTO/), [IGVFFI6454ELZI](/sequence-files/IGVFFI6454ELZI/), [IGVFFI2354AEWB](/sequence-files/IGVFFI2354AEWB/), [IGVFFI8600RPOF](/sequence-files/IGVFFI8600RPOF/), [IGVFFI1456WJRX](/sequence-files/IGVFFI1456WJRX/), [IGVFFI8595AITP](/sequence-files/IGVFFI8595AITP/), [IGVFFI1814KYRM](/sequence-files/IGVFFI1814KYRM/), [IGVFFI2994ZZMR](/sequence-files/IGVFFI2994ZZMR/), [IGVFFI1565TBUV](/sequence-files/IGVFFI1565TBUV/), [IGVFFI2460IBDC](/sequence-files/IGVFFI2460IBDC/), [IGVFFI9175RTOI](/sequence-files/IGVFFI9175RTOI/), [IGVFFI4738QTCW](/sequence-files/IGVFFI4738QTCW/), [IGVFFI6933HKOG](/sequence-files/IGVFFI6933HKOG/), [IGVFFI4463GCHO](/sequence-files/IGVFFI4463GCHO/), [IGVFFI8140XJEC](/sequence-files/IGVFFI8140XJEC/), [IGVFFI4878FNFC](/sequence-files/IGVFFI4878FNFC/), [IGVFFI5386LBQE](/sequence-files/IGVFFI5386LBQE/), [IGVFFI9022CFBG](/sequence-files/IGVFFI9022CFBG/), [IGVFFI4803IWND](/sequence-files/IGVFFI4803IWND/), [IGVFFI0308XYQL](/sequence-files/IGVFFI0308XYQL/), [IGVFFI8945XHDG](/sequence-files/IGVFFI8945XHDG/), [IGVFFI4946FMFY](/sequence-files/IGVFFI4946FMFY/), [IGVFFI2847OUAU](/sequence-files/IGVFFI2847OUAU/), [IGVFFI5827EQKF](/sequence-files/IGVFFI5827EQKF/), [IGVFFI3369JBRQ](/sequence-files/IGVFFI3369JBRQ/), [IGVFFI8084SBCW](/sequence-files/IGVFFI8084SBCW/), [IGVFFI6954JIGT](/sequence-files/IGVFFI6954JIGT/), [IGVFFI7208SQDY](/sequence-files/IGVFFI7208SQDY/), [IGVFFI4738IMYH](/sequence-files/IGVFFI4738IMYH/), [IGVFFI7433WSPS](/sequence-files/IGVFFI7433WSPS/) 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/IGVFDS4920QDPH/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS4920QDPH](/auxiliary-sets/IGVFDS4920QDPH/) has sequence file(s) [IGVFFI0689DCGL](/sequence-files/IGVFFI0689DCGL/), [IGVFFI3663MZAM](/sequence-files/IGVFFI3663MZAM/), [IGVFFI8824DFMJ](/sequence-files/IGVFFI8824DFMJ/), [IGVFFI3454DKAF](/sequence-files/IGVFFI3454DKAF/), [IGVFFI8240MXWF](/sequence-files/IGVFFI8240MXWF/), [IGVFFI3159FCSV](/sequence-files/IGVFFI3159FCSV/), [IGVFFI8073MEFZ](/sequence-files/IGVFFI8073MEFZ/), [IGVFFI8158ZOSQ](/sequence-files/IGVFFI8158ZOSQ/), [IGVFFI3429UOCE](/sequence-files/IGVFFI3429UOCE/), [IGVFFI8054NIXV](/sequence-files/IGVFFI8054NIXV/), [IGVFFI4228DTGP](/sequence-files/IGVFFI4228DTGP/), [IGVFFI8776UIEY](/sequence-files/IGVFFI8776UIEY/), [IGVFFI5231YNFI](/sequence-files/IGVFFI5231YNFI/), [IGVFFI6995XLQZ](/sequence-files/IGVFFI6995XLQZ/), [IGVFFI8826ESGW](/sequence-files/IGVFFI8826ESGW/), [IGVFFI5410XGYG](/sequence-files/IGVFFI5410XGYG/), [IGVFFI7367RFXB](/sequence-files/IGVFFI7367RFXB/), [IGVFFI2720ZSWR](/sequence-files/IGVFFI2720ZSWR/), [IGVFFI5610OGTO](/sequence-files/IGVFFI5610OGTO/), [IGVFFI6454ELZI](/sequence-files/IGVFFI6454ELZI/), [IGVFFI2354AEWB](/sequence-files/IGVFFI2354AEWB/), [IGVFFI8600RPOF](/sequence-files/IGVFFI8600RPOF/), [IGVFFI1456WJRX](/sequence-files/IGVFFI1456WJRX/), [IGVFFI8595AITP](/sequence-files/IGVFFI8595AITP/), [IGVFFI1814KYRM](/sequence-files/IGVFFI1814KYRM/), [IGVFFI2994ZZMR](/sequence-files/IGVFFI2994ZZMR/), [IGVFFI1565TBUV](/sequence-files/IGVFFI1565TBUV/), [IGVFFI2460IBDC](/sequence-files/IGVFFI2460IBDC/), [IGVFFI9175RTOI](/sequence-files/IGVFFI9175RTOI/), [IGVFFI4738QTCW](/sequence-files/IGVFFI4738QTCW/), [IGVFFI6933HKOG](/sequence-files/IGVFFI6933HKOG/), [IGVFFI4463GCHO](/sequence-files/IGVFFI4463GCHO/), [IGVFFI8140XJEC](/sequence-files/IGVFFI8140XJEC/), [IGVFFI4878FNFC](/sequence-files/IGVFFI4878FNFC/), [IGVFFI5386LBQE](/sequence-files/IGVFFI5386LBQE/), [IGVFFI9022CFBG](/sequence-files/IGVFFI9022CFBG/), [IGVFFI4803IWND](/sequence-files/IGVFFI4803IWND/), [IGVFFI0308XYQL](/sequence-files/IGVFFI0308XYQL/), [IGVFFI8945XHDG](/sequence-files/IGVFFI8945XHDG/), [IGVFFI4946FMFY](/sequence-files/IGVFFI4946FMFY/), [IGVFFI2847OUAU](/sequence-files/IGVFFI2847OUAU/), [IGVFFI5827EQKF](/sequence-files/IGVFFI5827EQKF/), [IGVFFI3369JBRQ](/sequence-files/IGVFFI3369JBRQ/), [IGVFFI8084SBCW](/sequence-files/IGVFFI8084SBCW/), [IGVFFI6954JIGT](/sequence-files/IGVFFI6954JIGT/), [IGVFFI7208SQDY](/sequence-files/IGVFFI7208SQDY/), [IGVFFI4738IMYH](/sequence-files/IGVFFI4738IMYH/), [IGVFFI7433WSPS](/sequence-files/IGVFFI7433WSPS/) 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/IGVFDS4920QDPH/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS4920QDPH](/auxiliary-sets/IGVFDS4920QDPH/) 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/IGVFDS4920QDPH/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS4920QDPH/",
"accession": "IGVFDS4920QDPH",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-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": "2023-12-13T08:01:40.600417+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": "2023-12-20T23:07:16.815406+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3122QCVP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3122QCVP",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-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": "2023-12-13T08:33:53.808351+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": "abc8f6d3-0418-497a-83a9-8b2dd2b31396"
}