{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5704ISFI/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5704ISFI",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep1-BinD_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 [IGVFSM9226UZTE](/in-vitro-systems/IGVFSM9226UZTE/) 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/IGVFSM9226UZTE/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS5704ISFI](/measurement-sets/IGVFDS5704ISFI/) has in progress subobject auxiliary set [IGVFDS9796QHGM](/auxiliary-sets/IGVFDS9796QHGM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS5704ISFI/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS9796QHGM](/auxiliary-sets/IGVFDS9796QHGM/) has sequence file(s): [IGVFFI6553BZFV](/sequence-files/IGVFFI6553BZFV/), [IGVFFI9423VKHN](/sequence-files/IGVFFI9423VKHN/), [IGVFFI4079EOFQ](/sequence-files/IGVFFI4079EOFQ/), [IGVFFI5141WKEV](/sequence-files/IGVFFI5141WKEV/), [IGVFFI6558JYNG](/sequence-files/IGVFFI6558JYNG/), [IGVFFI7975NHEB](/sequence-files/IGVFFI7975NHEB/), [IGVFFI4370EHQW](/sequence-files/IGVFFI4370EHQW/), [IGVFFI8868GOPR](/sequence-files/IGVFFI8868GOPR/), [IGVFFI5860XGDV](/sequence-files/IGVFFI5860XGDV/), [IGVFFI5304CPBL](/sequence-files/IGVFFI5304CPBL/), [IGVFFI0171OZDZ](/sequence-files/IGVFFI0171OZDZ/), [IGVFFI4462TSLM](/sequence-files/IGVFFI4462TSLM/), [IGVFFI4359TUGO](/sequence-files/IGVFFI4359TUGO/), [IGVFFI2147RQPO](/sequence-files/IGVFFI2147RQPO/), [IGVFFI2843ESSU](/sequence-files/IGVFFI2843ESSU/), [IGVFFI5277ZRIE](/sequence-files/IGVFFI5277ZRIE/), [IGVFFI5140USUU](/sequence-files/IGVFFI5140USUU/), [IGVFFI5208MYFF](/sequence-files/IGVFFI5208MYFF/), [IGVFFI2554UETT](/sequence-files/IGVFFI2554UETT/), [IGVFFI8039TKUY](/sequence-files/IGVFFI8039TKUY/), [IGVFFI0422PHBM](/sequence-files/IGVFFI0422PHBM/), [IGVFFI2083YHGP](/sequence-files/IGVFFI2083YHGP/), [IGVFFI1505XVNP](/sequence-files/IGVFFI1505XVNP/), [IGVFFI7734DPOO](/sequence-files/IGVFFI7734DPOO/), [IGVFFI6213BLQG](/sequence-files/IGVFFI6213BLQG/), [IGVFFI6306HZBJ](/sequence-files/IGVFFI6306HZBJ/), [IGVFFI9929QQXR](/sequence-files/IGVFFI9929QQXR/), [IGVFFI3493CGNU](/sequence-files/IGVFFI3493CGNU/), [IGVFFI5212WAGE](/sequence-files/IGVFFI5212WAGE/), [IGVFFI0848GDNO](/sequence-files/IGVFFI0848GDNO/), [IGVFFI4324CZKV](/sequence-files/IGVFFI4324CZKV/), [IGVFFI2399VDEC](/sequence-files/IGVFFI2399VDEC/), [IGVFFI3684LSEW](/sequence-files/IGVFFI3684LSEW/), [IGVFFI7671ZFQL](/sequence-files/IGVFFI7671ZFQL/), [IGVFFI9334DIMV](/sequence-files/IGVFFI9334DIMV/), [IGVFFI4161KMOW](/sequence-files/IGVFFI4161KMOW/), [IGVFFI7599ABTQ](/sequence-files/IGVFFI7599ABTQ/), [IGVFFI5814CUST](/sequence-files/IGVFFI5814CUST/), [IGVFFI3715ITHN](/sequence-files/IGVFFI3715ITHN/), [IGVFFI3689PCPR](/sequence-files/IGVFFI3689PCPR/), [IGVFFI6637MEWE](/sequence-files/IGVFFI6637MEWE/), [IGVFFI7883GSUO](/sequence-files/IGVFFI7883GSUO/), [IGVFFI1883DKHL](/sequence-files/IGVFFI1883DKHL/), [IGVFFI6204YQGV](/sequence-files/IGVFFI6204YQGV/), [IGVFFI9286RTEL](/sequence-files/IGVFFI9286RTEL/), [IGVFFI0197BRAF](/sequence-files/IGVFFI0197BRAF/), [IGVFFI1014PBZO](/sequence-files/IGVFFI1014PBZO/), [IGVFFI3194UDCC](/sequence-files/IGVFFI3194UDCC/) 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/IGVFDS9796QHGM/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5704ISFI](/measurement-sets/IGVFDS5704ISFI/) 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/IGVFDS5704ISFI/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS9796QHGM](/auxiliary-sets/IGVFDS9796QHGM/) has sequence file(s) [IGVFFI6553BZFV](/sequence-files/IGVFFI6553BZFV/), [IGVFFI9423VKHN](/sequence-files/IGVFFI9423VKHN/), [IGVFFI4079EOFQ](/sequence-files/IGVFFI4079EOFQ/), [IGVFFI5141WKEV](/sequence-files/IGVFFI5141WKEV/), [IGVFFI6558JYNG](/sequence-files/IGVFFI6558JYNG/), [IGVFFI7975NHEB](/sequence-files/IGVFFI7975NHEB/), [IGVFFI4370EHQW](/sequence-files/IGVFFI4370EHQW/), [IGVFFI8868GOPR](/sequence-files/IGVFFI8868GOPR/), [IGVFFI5860XGDV](/sequence-files/IGVFFI5860XGDV/), [IGVFFI5304CPBL](/sequence-files/IGVFFI5304CPBL/), [IGVFFI0171OZDZ](/sequence-files/IGVFFI0171OZDZ/), [IGVFFI4462TSLM](/sequence-files/IGVFFI4462TSLM/), [IGVFFI4359TUGO](/sequence-files/IGVFFI4359TUGO/), [IGVFFI2147RQPO](/sequence-files/IGVFFI2147RQPO/), [IGVFFI2843ESSU](/sequence-files/IGVFFI2843ESSU/), [IGVFFI5277ZRIE](/sequence-files/IGVFFI5277ZRIE/), [IGVFFI5140USUU](/sequence-files/IGVFFI5140USUU/), [IGVFFI5208MYFF](/sequence-files/IGVFFI5208MYFF/), [IGVFFI2554UETT](/sequence-files/IGVFFI2554UETT/), [IGVFFI8039TKUY](/sequence-files/IGVFFI8039TKUY/), [IGVFFI0422PHBM](/sequence-files/IGVFFI0422PHBM/), [IGVFFI2083YHGP](/sequence-files/IGVFFI2083YHGP/), [IGVFFI1505XVNP](/sequence-files/IGVFFI1505XVNP/), [IGVFFI7734DPOO](/sequence-files/IGVFFI7734DPOO/), [IGVFFI6213BLQG](/sequence-files/IGVFFI6213BLQG/), [IGVFFI6306HZBJ](/sequence-files/IGVFFI6306HZBJ/), [IGVFFI9929QQXR](/sequence-files/IGVFFI9929QQXR/), [IGVFFI3493CGNU](/sequence-files/IGVFFI3493CGNU/), [IGVFFI5212WAGE](/sequence-files/IGVFFI5212WAGE/), [IGVFFI0848GDNO](/sequence-files/IGVFFI0848GDNO/), [IGVFFI4324CZKV](/sequence-files/IGVFFI4324CZKV/), [IGVFFI2399VDEC](/sequence-files/IGVFFI2399VDEC/), [IGVFFI3684LSEW](/sequence-files/IGVFFI3684LSEW/), [IGVFFI7671ZFQL](/sequence-files/IGVFFI7671ZFQL/), [IGVFFI9334DIMV](/sequence-files/IGVFFI9334DIMV/), [IGVFFI4161KMOW](/sequence-files/IGVFFI4161KMOW/), [IGVFFI7599ABTQ](/sequence-files/IGVFFI7599ABTQ/), [IGVFFI5814CUST](/sequence-files/IGVFFI5814CUST/), [IGVFFI3715ITHN](/sequence-files/IGVFFI3715ITHN/), [IGVFFI3689PCPR](/sequence-files/IGVFFI3689PCPR/), [IGVFFI6637MEWE](/sequence-files/IGVFFI6637MEWE/), [IGVFFI7883GSUO](/sequence-files/IGVFFI7883GSUO/), [IGVFFI1883DKHL](/sequence-files/IGVFFI1883DKHL/), [IGVFFI6204YQGV](/sequence-files/IGVFFI6204YQGV/), [IGVFFI9286RTEL](/sequence-files/IGVFFI9286RTEL/), [IGVFFI0197BRAF](/sequence-files/IGVFFI0197BRAF/), [IGVFFI1014PBZO](/sequence-files/IGVFFI1014PBZO/), [IGVFFI3194UDCC](/sequence-files/IGVFFI3194UDCC/) 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/IGVFDS9796QHGM/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS9796QHGM](/auxiliary-sets/IGVFDS9796QHGM/) 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/IGVFDS9796QHGM/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS9796QHGM/",
"accession": "IGVFDS9796QHGM",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep1-BinD_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/IGVFDS4869FXYY/",
"accession": "IGVFDS4869FXYY",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-Jurkat-PE2_Exp2_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-12-13T08:48:03.662986+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1080XFGV/",
"accession": "IGVFDO1080XFGV",
"aliases": [
"igvf:donor_of_Jurkat"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "experimental data",
"files": [],
"input_file_set_for": [
"/analysis-sets/IGVFDS6299IJHG/"
],
"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": "2023-12-20T23:08:43.483649+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9226UZTE/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9226UZTE",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep1-BinD"
],
"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_0002796/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:Jurkat"
],
"status": "released",
"summary": "Jurkat",
"term_name": "Jurkat"
}
],
"status": "released",
"summary": "Jurkat cell line, male, Homo sapiens (sorting details: FACS bin for 76-100% 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": "2023-12-13T09:19:39.680404+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": "e6050ebf-9c50-4aad-9f6e-bdfb12be236f"
}