{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4363PDBQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4363PDBQ",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinA_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 [IGVFSM7022AZSZ](/in-vitro-systems/IGVFSM7022AZSZ/) 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/IGVFSM7022AZSZ/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS4363PDBQ](/measurement-sets/IGVFDS4363PDBQ/) has in progress subobject auxiliary set [IGVFDS1895YQOO](/auxiliary-sets/IGVFDS1895YQOO/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS4363PDBQ/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS1895YQOO](/auxiliary-sets/IGVFDS1895YQOO/) has sequence file(s): [IGVFFI0688UTKC](/sequence-files/IGVFFI0688UTKC/), [IGVFFI8158ZGYG](/sequence-files/IGVFFI8158ZGYG/), [IGVFFI5096XZQL](/sequence-files/IGVFFI5096XZQL/), [IGVFFI7873TDXV](/sequence-files/IGVFFI7873TDXV/), [IGVFFI3479TMIU](/sequence-files/IGVFFI3479TMIU/), [IGVFFI3526JNXX](/sequence-files/IGVFFI3526JNXX/), [IGVFFI8404FFCL](/sequence-files/IGVFFI8404FFCL/), [IGVFFI0648NHIY](/sequence-files/IGVFFI0648NHIY/), [IGVFFI7716SPRQ](/sequence-files/IGVFFI7716SPRQ/), [IGVFFI6858LVPD](/sequence-files/IGVFFI6858LVPD/), [IGVFFI3993QHHH](/sequence-files/IGVFFI3993QHHH/), [IGVFFI8425VACP](/sequence-files/IGVFFI8425VACP/), [IGVFFI4658GCRC](/sequence-files/IGVFFI4658GCRC/), [IGVFFI6523BPVA](/sequence-files/IGVFFI6523BPVA/), [IGVFFI8613ZFWT](/sequence-files/IGVFFI8613ZFWT/), [IGVFFI3504WMBE](/sequence-files/IGVFFI3504WMBE/), [IGVFFI3969QTOQ](/sequence-files/IGVFFI3969QTOQ/), [IGVFFI3292NNDU](/sequence-files/IGVFFI3292NNDU/), [IGVFFI2704ZQKL](/sequence-files/IGVFFI2704ZQKL/), [IGVFFI5773DLCD](/sequence-files/IGVFFI5773DLCD/), [IGVFFI3795KIIZ](/sequence-files/IGVFFI3795KIIZ/), [IGVFFI9448GSSH](/sequence-files/IGVFFI9448GSSH/), [IGVFFI7259SQNP](/sequence-files/IGVFFI7259SQNP/), [IGVFFI0073HMFZ](/sequence-files/IGVFFI0073HMFZ/), [IGVFFI5891IEQF](/sequence-files/IGVFFI5891IEQF/), [IGVFFI7637FDZV](/sequence-files/IGVFFI7637FDZV/), [IGVFFI0509PMXO](/sequence-files/IGVFFI0509PMXO/), [IGVFFI0483XIJN](/sequence-files/IGVFFI0483XIJN/), [IGVFFI6691NXNV](/sequence-files/IGVFFI6691NXNV/), [IGVFFI9897KDBL](/sequence-files/IGVFFI9897KDBL/), [IGVFFI2938MMVH](/sequence-files/IGVFFI2938MMVH/), [IGVFFI7590MSKR](/sequence-files/IGVFFI7590MSKR/), [IGVFFI1911GKQJ](/sequence-files/IGVFFI1911GKQJ/), [IGVFFI3474HVUB](/sequence-files/IGVFFI3474HVUB/), [IGVFFI5942ENOH](/sequence-files/IGVFFI5942ENOH/), [IGVFFI0691LITJ](/sequence-files/IGVFFI0691LITJ/), [IGVFFI3586YWZR](/sequence-files/IGVFFI3586YWZR/), [IGVFFI0008OYBZ](/sequence-files/IGVFFI0008OYBZ/), [IGVFFI4159WQPT](/sequence-files/IGVFFI4159WQPT/), [IGVFFI9762JQQT](/sequence-files/IGVFFI9762JQQT/), [IGVFFI7267JDSJ](/sequence-files/IGVFFI7267JDSJ/), [IGVFFI7811YIDZ](/sequence-files/IGVFFI7811YIDZ/), [IGVFFI7332KNDG](/sequence-files/IGVFFI7332KNDG/), [IGVFFI3738GIKS](/sequence-files/IGVFFI3738GIKS/), [IGVFFI8900JTPL](/sequence-files/IGVFFI8900JTPL/), [IGVFFI3658IWSQ](/sequence-files/IGVFFI3658IWSQ/), [IGVFFI1656DKBA](/sequence-files/IGVFFI1656DKBA/), [IGVFFI3522WZLX](/sequence-files/IGVFFI3522WZLX/) 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/IGVFDS1895YQOO/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4363PDBQ](/measurement-sets/IGVFDS4363PDBQ/) 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/IGVFDS4363PDBQ/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS1895YQOO](/auxiliary-sets/IGVFDS1895YQOO/) has sequence file(s) [IGVFFI0688UTKC](/sequence-files/IGVFFI0688UTKC/), [IGVFFI8158ZGYG](/sequence-files/IGVFFI8158ZGYG/), [IGVFFI5096XZQL](/sequence-files/IGVFFI5096XZQL/), [IGVFFI7873TDXV](/sequence-files/IGVFFI7873TDXV/), [IGVFFI3479TMIU](/sequence-files/IGVFFI3479TMIU/), [IGVFFI3526JNXX](/sequence-files/IGVFFI3526JNXX/), [IGVFFI8404FFCL](/sequence-files/IGVFFI8404FFCL/), [IGVFFI0648NHIY](/sequence-files/IGVFFI0648NHIY/), [IGVFFI7716SPRQ](/sequence-files/IGVFFI7716SPRQ/), [IGVFFI6858LVPD](/sequence-files/IGVFFI6858LVPD/), [IGVFFI3993QHHH](/sequence-files/IGVFFI3993QHHH/), [IGVFFI8425VACP](/sequence-files/IGVFFI8425VACP/), [IGVFFI4658GCRC](/sequence-files/IGVFFI4658GCRC/), [IGVFFI6523BPVA](/sequence-files/IGVFFI6523BPVA/), [IGVFFI8613ZFWT](/sequence-files/IGVFFI8613ZFWT/), [IGVFFI3504WMBE](/sequence-files/IGVFFI3504WMBE/), [IGVFFI3969QTOQ](/sequence-files/IGVFFI3969QTOQ/), [IGVFFI3292NNDU](/sequence-files/IGVFFI3292NNDU/), [IGVFFI2704ZQKL](/sequence-files/IGVFFI2704ZQKL/), [IGVFFI5773DLCD](/sequence-files/IGVFFI5773DLCD/), [IGVFFI3795KIIZ](/sequence-files/IGVFFI3795KIIZ/), [IGVFFI9448GSSH](/sequence-files/IGVFFI9448GSSH/), [IGVFFI7259SQNP](/sequence-files/IGVFFI7259SQNP/), [IGVFFI0073HMFZ](/sequence-files/IGVFFI0073HMFZ/), [IGVFFI5891IEQF](/sequence-files/IGVFFI5891IEQF/), [IGVFFI7637FDZV](/sequence-files/IGVFFI7637FDZV/), [IGVFFI0509PMXO](/sequence-files/IGVFFI0509PMXO/), [IGVFFI0483XIJN](/sequence-files/IGVFFI0483XIJN/), [IGVFFI6691NXNV](/sequence-files/IGVFFI6691NXNV/), [IGVFFI9897KDBL](/sequence-files/IGVFFI9897KDBL/), [IGVFFI2938MMVH](/sequence-files/IGVFFI2938MMVH/), [IGVFFI7590MSKR](/sequence-files/IGVFFI7590MSKR/), [IGVFFI1911GKQJ](/sequence-files/IGVFFI1911GKQJ/), [IGVFFI3474HVUB](/sequence-files/IGVFFI3474HVUB/), [IGVFFI5942ENOH](/sequence-files/IGVFFI5942ENOH/), [IGVFFI0691LITJ](/sequence-files/IGVFFI0691LITJ/), [IGVFFI3586YWZR](/sequence-files/IGVFFI3586YWZR/), [IGVFFI0008OYBZ](/sequence-files/IGVFFI0008OYBZ/), [IGVFFI4159WQPT](/sequence-files/IGVFFI4159WQPT/), [IGVFFI9762JQQT](/sequence-files/IGVFFI9762JQQT/), [IGVFFI7267JDSJ](/sequence-files/IGVFFI7267JDSJ/), [IGVFFI7811YIDZ](/sequence-files/IGVFFI7811YIDZ/), [IGVFFI7332KNDG](/sequence-files/IGVFFI7332KNDG/), [IGVFFI3738GIKS](/sequence-files/IGVFFI3738GIKS/), [IGVFFI8900JTPL](/sequence-files/IGVFFI8900JTPL/), [IGVFFI3658IWSQ](/sequence-files/IGVFFI3658IWSQ/), [IGVFFI1656DKBA](/sequence-files/IGVFFI1656DKBA/), [IGVFFI3522WZLX](/sequence-files/IGVFFI3522WZLX/) 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/IGVFDS1895YQOO/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS1895YQOO](/auxiliary-sets/IGVFDS1895YQOO/) 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/IGVFDS1895YQOO/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS1895YQOO/",
"accession": "IGVFDS1895YQOO",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinA_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": "2023-12-13T08:01:44.893025+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": "2023-12-20T23:07:15.116933+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7022AZSZ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7022AZSZ",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinA"
],
"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 0-25% 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": "2023-12-13T08:58:40.646423+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": "fe739718-a398-4e5c-b7b5-4d95497c90ad"
}