{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7378QBUS/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7378QBUS",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-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 measurement set [IGVFDS7378QBUS](/measurement-sets/IGVFDS7378QBUS/) has in progress subobject auxiliary set [IGVFDS5116HXHL](/auxiliary-sets/IGVFDS5116HXHL/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS7378QBUS/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM3068WOLM](/in-vitro-systems/IGVFSM3068WOLM/) 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/IGVFSM3068WOLM/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS5116HXHL](/auxiliary-sets/IGVFDS5116HXHL/) has sequence file(s): [IGVFFI0825KMZO](/sequence-files/IGVFFI0825KMZO/), [IGVFFI5498TYRV](/sequence-files/IGVFFI5498TYRV/), [IGVFFI1870FBGA](/sequence-files/IGVFFI1870FBGA/), [IGVFFI6285ILUX](/sequence-files/IGVFFI6285ILUX/), [IGVFFI2301ERHJ](/sequence-files/IGVFFI2301ERHJ/), [IGVFFI0872NGUU](/sequence-files/IGVFFI0872NGUU/), [IGVFFI3184XGRQ](/sequence-files/IGVFFI3184XGRQ/), [IGVFFI3685RHYH](/sequence-files/IGVFFI3685RHYH/), [IGVFFI1247CTXE](/sequence-files/IGVFFI1247CTXE/), [IGVFFI2081WAWT](/sequence-files/IGVFFI2081WAWT/), [IGVFFI2050DMEZ](/sequence-files/IGVFFI2050DMEZ/), [IGVFFI1190ZXKK](/sequence-files/IGVFFI1190ZXKK/), [IGVFFI6700DMWS](/sequence-files/IGVFFI6700DMWS/), [IGVFFI7554QBFB](/sequence-files/IGVFFI7554QBFB/), [IGVFFI5732CDSO](/sequence-files/IGVFFI5732CDSO/), [IGVFFI0771XGBN](/sequence-files/IGVFFI0771XGBN/), [IGVFFI2367JHST](/sequence-files/IGVFFI2367JHST/), [IGVFFI6765QZSM](/sequence-files/IGVFFI6765QZSM/), [IGVFFI6918JUFX](/sequence-files/IGVFFI6918JUFX/), [IGVFFI5824BTSG](/sequence-files/IGVFFI5824BTSG/), [IGVFFI1677OISD](/sequence-files/IGVFFI1677OISD/), [IGVFFI8403BEFW](/sequence-files/IGVFFI8403BEFW/), [IGVFFI5038EGNV](/sequence-files/IGVFFI5038EGNV/), [IGVFFI0349GQUV](/sequence-files/IGVFFI0349GQUV/), [IGVFFI3105NPCJ](/sequence-files/IGVFFI3105NPCJ/), [IGVFFI0147UHER](/sequence-files/IGVFFI0147UHER/), [IGVFFI7988OJTW](/sequence-files/IGVFFI7988OJTW/), [IGVFFI8167GTDR](/sequence-files/IGVFFI8167GTDR/), [IGVFFI9267IJCA](/sequence-files/IGVFFI9267IJCA/), [IGVFFI5203GEWH](/sequence-files/IGVFFI5203GEWH/), [IGVFFI3535HXAP](/sequence-files/IGVFFI3535HXAP/), [IGVFFI3597BDBH](/sequence-files/IGVFFI3597BDBH/), [IGVFFI6543HXEZ](/sequence-files/IGVFFI6543HXEZ/), [IGVFFI7387NLGV](/sequence-files/IGVFFI7387NLGV/), [IGVFFI3956EYUL](/sequence-files/IGVFFI3956EYUL/), [IGVFFI5070HSEG](/sequence-files/IGVFFI5070HSEG/), [IGVFFI2620GXZT](/sequence-files/IGVFFI2620GXZT/), [IGVFFI1744AVXC](/sequence-files/IGVFFI1744AVXC/), [IGVFFI3698ONCL](/sequence-files/IGVFFI3698ONCL/), [IGVFFI5360BAXC](/sequence-files/IGVFFI5360BAXC/), [IGVFFI1017QKKQ](/sequence-files/IGVFFI1017QKKQ/), [IGVFFI8421PLYI](/sequence-files/IGVFFI8421PLYI/), [IGVFFI5143ASFN](/sequence-files/IGVFFI5143ASFN/), [IGVFFI7406XZOP](/sequence-files/IGVFFI7406XZOP/), [IGVFFI9359DPME](/sequence-files/IGVFFI9359DPME/), [IGVFFI8887IXYI](/sequence-files/IGVFFI8887IXYI/), [IGVFFI4173YXPL](/sequence-files/IGVFFI4173YXPL/), [IGVFFI0926TEIU](/sequence-files/IGVFFI0926TEIU/) 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/IGVFDS5116HXHL/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7378QBUS](/measurement-sets/IGVFDS7378QBUS/) 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/IGVFDS7378QBUS/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS5116HXHL](/auxiliary-sets/IGVFDS5116HXHL/) has sequence file(s) [IGVFFI0825KMZO](/sequence-files/IGVFFI0825KMZO/), [IGVFFI5498TYRV](/sequence-files/IGVFFI5498TYRV/), [IGVFFI1870FBGA](/sequence-files/IGVFFI1870FBGA/), [IGVFFI6285ILUX](/sequence-files/IGVFFI6285ILUX/), [IGVFFI2301ERHJ](/sequence-files/IGVFFI2301ERHJ/), [IGVFFI0872NGUU](/sequence-files/IGVFFI0872NGUU/), [IGVFFI3184XGRQ](/sequence-files/IGVFFI3184XGRQ/), [IGVFFI3685RHYH](/sequence-files/IGVFFI3685RHYH/), [IGVFFI1247CTXE](/sequence-files/IGVFFI1247CTXE/), [IGVFFI2081WAWT](/sequence-files/IGVFFI2081WAWT/), [IGVFFI2050DMEZ](/sequence-files/IGVFFI2050DMEZ/), [IGVFFI1190ZXKK](/sequence-files/IGVFFI1190ZXKK/), [IGVFFI6700DMWS](/sequence-files/IGVFFI6700DMWS/), [IGVFFI7554QBFB](/sequence-files/IGVFFI7554QBFB/), [IGVFFI5732CDSO](/sequence-files/IGVFFI5732CDSO/), [IGVFFI0771XGBN](/sequence-files/IGVFFI0771XGBN/), [IGVFFI2367JHST](/sequence-files/IGVFFI2367JHST/), [IGVFFI6765QZSM](/sequence-files/IGVFFI6765QZSM/), [IGVFFI6918JUFX](/sequence-files/IGVFFI6918JUFX/), [IGVFFI5824BTSG](/sequence-files/IGVFFI5824BTSG/), [IGVFFI1677OISD](/sequence-files/IGVFFI1677OISD/), [IGVFFI8403BEFW](/sequence-files/IGVFFI8403BEFW/), [IGVFFI5038EGNV](/sequence-files/IGVFFI5038EGNV/), [IGVFFI0349GQUV](/sequence-files/IGVFFI0349GQUV/), [IGVFFI3105NPCJ](/sequence-files/IGVFFI3105NPCJ/), [IGVFFI0147UHER](/sequence-files/IGVFFI0147UHER/), [IGVFFI7988OJTW](/sequence-files/IGVFFI7988OJTW/), [IGVFFI8167GTDR](/sequence-files/IGVFFI8167GTDR/), [IGVFFI9267IJCA](/sequence-files/IGVFFI9267IJCA/), [IGVFFI5203GEWH](/sequence-files/IGVFFI5203GEWH/), [IGVFFI3535HXAP](/sequence-files/IGVFFI3535HXAP/), [IGVFFI3597BDBH](/sequence-files/IGVFFI3597BDBH/), [IGVFFI6543HXEZ](/sequence-files/IGVFFI6543HXEZ/), [IGVFFI7387NLGV](/sequence-files/IGVFFI7387NLGV/), [IGVFFI3956EYUL](/sequence-files/IGVFFI3956EYUL/), [IGVFFI5070HSEG](/sequence-files/IGVFFI5070HSEG/), [IGVFFI2620GXZT](/sequence-files/IGVFFI2620GXZT/), [IGVFFI1744AVXC](/sequence-files/IGVFFI1744AVXC/), [IGVFFI3698ONCL](/sequence-files/IGVFFI3698ONCL/), [IGVFFI5360BAXC](/sequence-files/IGVFFI5360BAXC/), [IGVFFI1017QKKQ](/sequence-files/IGVFFI1017QKKQ/), [IGVFFI8421PLYI](/sequence-files/IGVFFI8421PLYI/), [IGVFFI5143ASFN](/sequence-files/IGVFFI5143ASFN/), [IGVFFI7406XZOP](/sequence-files/IGVFFI7406XZOP/), [IGVFFI9359DPME](/sequence-files/IGVFFI9359DPME/), [IGVFFI8887IXYI](/sequence-files/IGVFFI8887IXYI/), [IGVFFI4173YXPL](/sequence-files/IGVFFI4173YXPL/), [IGVFFI0926TEIU](/sequence-files/IGVFFI0926TEIU/) 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/IGVFDS5116HXHL/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS5116HXHL](/auxiliary-sets/IGVFDS5116HXHL/) 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/IGVFDS5116HXHL/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS5116HXHL/",
"accession": "IGVFDS5116HXHL",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-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/IGVFDS5128CXIS/",
"accession": "IGVFDS5128CXIS",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-12-13T08:01:38.685226+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": "2023-12-20T23:07:42.673722+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3068WOLM/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3068WOLM",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-BinB"
],
"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 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": "2023-12-13T08:25:22.136203+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": "ceb5121c-a52d-40b1-b168-ef5578a2da08"
}