{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5128CXIS/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5128CXIS",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS5128CXIS](/measurement-sets/IGVFDS5128CXIS/) has sequence file(s) [IGVFFI8992CXFT](/sequence-files/IGVFFI8992CXFT/), [IGVFFI9984TILJ](/sequence-files/IGVFFI9984TILJ/), [IGVFFI1898QYOM](/sequence-files/IGVFFI1898QYOM/), [IGVFFI5860PVJQ](/sequence-files/IGVFFI5860PVJQ/), [IGVFFI1798AJTL](/sequence-files/IGVFFI1798AJTL/), [IGVFFI3449WZQF](/sequence-files/IGVFFI3449WZQF/), [IGVFFI8823JOUV](/sequence-files/IGVFFI8823JOUV/), [IGVFFI1771FPVE](/sequence-files/IGVFFI1771FPVE/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS5128CXIS/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5128CXIS](/measurement-sets/IGVFDS5128CXIS/) has sequence file(s): [IGVFFI8992CXFT](/sequence-files/IGVFFI8992CXFT/), [IGVFFI9984TILJ](/sequence-files/IGVFFI9984TILJ/), [IGVFFI1898QYOM](/sequence-files/IGVFFI1898QYOM/), [IGVFFI5860PVJQ](/sequence-files/IGVFFI5860PVJQ/), [IGVFFI1798AJTL](/sequence-files/IGVFFI1798AJTL/), [IGVFFI3449WZQF](/sequence-files/IGVFFI3449WZQF/), [IGVFFI8823JOUV](/sequence-files/IGVFFI8823JOUV/), [IGVFFI1771FPVE](/sequence-files/IGVFFI1771FPVE/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS5128CXIS/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5128CXIS](/measurement-sets/IGVFDS5128CXIS/) 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": 40,
"level_name": "WARNING",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS5128CXIS/"
},
{
"category": "missing targeted genes",
"detail": "Measurement set [IGVFDS5128CXIS](/measurement-sets/IGVFDS5128CXIS/) has no `targeted_genes`. ChIP-seq and CRISPR flow cytometry assays are expected to specify targeted gene(s).",
"level": 40,
"level_name": "WARNING",
"name": "audit_targeted_genes",
"path": "/measurement-sets/IGVFDS5128CXIS/"
}
]
},
"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_for": [
{
"@id": "/measurement-sets/IGVFDS7230BLHQ/",
"accession": "IGVFDS7230BLHQ",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep3-BinD_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6069DTLX/",
"accession": "IGVFDS6069DTLX",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep4-BinB_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4188FAAP/",
"accession": "IGVFDS4188FAAP",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep4-FACS_Input_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS3508UNRE/",
"accession": "IGVFDS3508UNRE",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinA_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS0176OXWE/",
"accession": "IGVFDS0176OXWE",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinB_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS5338RAZZ/",
"accession": "IGVFDS5338RAZZ",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinC_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8099KDSE/",
"accession": "IGVFDS8099KDSE",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep1-BinD_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6957VHOD/",
"accession": "IGVFDS6957VHOD",
"aliases": [
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],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6252SSYB/",
"accession": "IGVFDS6252SSYB",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep3-BinB_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS0839SQRJ/",
"accession": "IGVFDS0839SQRJ",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep3-BinC_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS5795QOPU/",
"accession": "IGVFDS5795QOPU",
"aliases": [
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],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS7378QBUS/",
"accession": "IGVFDS7378QBUS",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-BinB_AmpliconSequencing"
],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8933DNXM/",
"accession": "IGVFDS8933DNXM",
"aliases": [
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],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS2940LDCT/",
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"aliases": [
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],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4141QOFR/",
"accession": "IGVFDS4141QOFR",
"aliases": [
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],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6384OLQB/",
"accession": "IGVFDS6384OLQB",
"aliases": [
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],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS2294QFQV/",
"accession": "IGVFDS2294QFQV",
"aliases": [
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],
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS3326NVFS/",
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],
"status": "released"
},
{
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"status": "released"
},
{
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],
"status": "released"
},
{
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],
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},
{
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],
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},
{
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],
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},
{
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},
{
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},
{
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],
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},
{
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},
{
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},
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],
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},
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},
{
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{
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{
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}
],
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{
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"status": "released",
"taxa": "Homo sapiens"
}
],
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},
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},
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},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8823JOUV/",
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],
"content_type": "reads",
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"creation_timestamp": "2023-12-13T15:01:45.293393+00:00",
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"@id": "/sequence-files/IGVFFI1771FPVE/",
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],
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"creation_timestamp": "2023-12-13T16:05:29.264512+00:00",
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}
],
"input_for": [
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],
"lab": {
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"title": "Jesse Engreitz, Stanford"
},
"notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set. This measurement set previously used Variant FlowFISH as a preferred_assay_title, but this enum is now removed. So it has been defaulted to Variant-EFFECTS.",
"preferred_assay_title": "Variant-EFFECTS",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"release_timestamp": "2023-12-20T23:07:56.546430+00:00",
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{
"@id": "/in-vitro-systems/IGVFSM3211UEWZ/",
"@type": [
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"Biosample",
"Sample",
"Item"
],
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],
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],
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{
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"modality": "prime editing",
"status": "released"
}
],
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"@type": [
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"OntologyTerm",
"Item"
],
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"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)",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
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"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-13T08:17:19.736198+00:00",
"summary": "untransfected prime editing Variant-EFFECTS",
"uuid": "fb47792f-c0be-488b-84bd-c23a65c154a1"
}