{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0629YEMD/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0629YEMD",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-FACS_Input_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 [IGVFSM6276DPKS](/in-vitro-systems/IGVFSM6276DPKS/) has in progress subobject construct library set [IGVFDS6982DESN](/construct-library-sets/IGVFDS6982DESN/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM6276DPKS/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0629YEMD](/measurement-sets/IGVFDS0629YEMD/) has in progress subobject auxiliary set [IGVFDS8492QXPJ](/auxiliary-sets/IGVFDS8492QXPJ/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0629YEMD/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8492QXPJ](/auxiliary-sets/IGVFDS8492QXPJ/) has sequence file(s) [IGVFFI6469SVUU](/sequence-files/IGVFFI6469SVUU/), [IGVFFI5754KELW](/sequence-files/IGVFFI5754KELW/), [IGVFFI9357QJYS](/sequence-files/IGVFFI9357QJYS/), [IGVFFI9971VICM](/sequence-files/IGVFFI9971VICM/), [IGVFFI9597PKII](/sequence-files/IGVFFI9597PKII/), [IGVFFI3762ADST](/sequence-files/IGVFFI3762ADST/), [IGVFFI5022GHUD](/sequence-files/IGVFFI5022GHUD/), [IGVFFI6287AEUR](/sequence-files/IGVFFI6287AEUR/), [IGVFFI0201OZPG](/sequence-files/IGVFFI0201OZPG/), [IGVFFI5824KSZO](/sequence-files/IGVFFI5824KSZO/), [IGVFFI8962GESX](/sequence-files/IGVFFI8962GESX/), [IGVFFI4961ZHSS](/sequence-files/IGVFFI4961ZHSS/), [IGVFFI1144DBOQ](/sequence-files/IGVFFI1144DBOQ/), [IGVFFI2124HSYU](/sequence-files/IGVFFI2124HSYU/), [IGVFFI9179IONQ](/sequence-files/IGVFFI9179IONQ/), [IGVFFI8491NCJR](/sequence-files/IGVFFI8491NCJR/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS8492QXPJ/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8492QXPJ](/auxiliary-sets/IGVFDS8492QXPJ/) has sequence file(s): [IGVFFI6469SVUU](/sequence-files/IGVFFI6469SVUU/), [IGVFFI5754KELW](/sequence-files/IGVFFI5754KELW/), [IGVFFI9357QJYS](/sequence-files/IGVFFI9357QJYS/), [IGVFFI9971VICM](/sequence-files/IGVFFI9971VICM/), [IGVFFI9597PKII](/sequence-files/IGVFFI9597PKII/), [IGVFFI3762ADST](/sequence-files/IGVFFI3762ADST/), [IGVFFI5022GHUD](/sequence-files/IGVFFI5022GHUD/), [IGVFFI6287AEUR](/sequence-files/IGVFFI6287AEUR/), [IGVFFI0201OZPG](/sequence-files/IGVFFI0201OZPG/), [IGVFFI5824KSZO](/sequence-files/IGVFFI5824KSZO/), [IGVFFI8962GESX](/sequence-files/IGVFFI8962GESX/), [IGVFFI4961ZHSS](/sequence-files/IGVFFI4961ZHSS/), [IGVFFI1144DBOQ](/sequence-files/IGVFFI1144DBOQ/), [IGVFFI2124HSYU](/sequence-files/IGVFFI2124HSYU/), [IGVFFI9179IONQ](/sequence-files/IGVFFI9179IONQ/), [IGVFFI8491NCJR](/sequence-files/IGVFFI8491NCJR/) 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/IGVFDS8492QXPJ/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0629YEMD](/measurement-sets/IGVFDS0629YEMD/) 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/IGVFDS0629YEMD/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS0629YEMD](/measurement-sets/IGVFDS0629YEMD/) has no `targeted_genes`. ChIP-seq and CRISPR flow cytometry assays are expected to specify targeted gene(s).",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_targeted_genes",
"path": "/measurement-sets/IGVFDS0629YEMD/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS8492QXPJ](/auxiliary-sets/IGVFDS8492QXPJ/) 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_for",
"path": "/auxiliary-sets/IGVFDS8492QXPJ/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8492QXPJ/",
"accession": "IGVFDS8492QXPJ",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-FACS_Input_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/IGVFDS5864UGFT/",
"accession": "IGVFDS5864UGFT",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:50:09.331561+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [],
"input_for": [
"/analysis-sets/IGVFDS3423PSID/"
],
"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": "2023-12-20T23:06:07.283202+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6276DPKS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6276DPKS",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-FACS_Input"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6982DESN/",
"accession": "IGVFDS6982DESN",
"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 modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "22",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T23:32:43.691970+00:00",
"summary": "prime editing Variant FlowFISH integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"uuid": "900eb589-eb3b-4cfc-81b2-9eaf7555b6b0"
}