{
"@context": "/terms/",
"@id": "/in-vitro-systems/IGVFSM6463YBYJ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6463YBYJ",
"age": "unknown",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinC"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM6463YBYJ](/in-vitro-systems/IGVFSM6463YBYJ/) 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/IGVFSM6463YBYJ/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing plasmid map",
"detail": "Construct library set [IGVFDS6982DESN](/construct-library-sets/IGVFDS6982DESN/) does not have a plasmid map attached in `documents`. Construct library sets are expected to be associated with a plasmid map document.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_construct_library_set_plasmid_map",
"path": "/construct-library-sets/IGVFDS6982DESN/"
},
{
"category": "missing guide RNA sequences",
"detail": "Construct library set [IGVFDS6982DESN](/construct-library-sets/IGVFDS6982DESN/) has no `integrated_content_files`. Guide libraries are expected to link to an integrated content file of guide RNA sequences.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_integrated_content_files",
"path": "/construct-library-sets/IGVFDS6982DESN/"
},
{
"category": "missing sequencing kit",
"detail": "Construct library set [IGVFDS6982DESN](/construct-library-sets/IGVFDS6982DESN/) has sequence file(s) [IGVFFI7000JWXA](/sequence-files/IGVFFI7000JWXA/), [IGVFFI5899AJIC](/sequence-files/IGVFFI5899AJIC/), [IGVFFI6383SCZF](/sequence-files/IGVFFI6383SCZF/) 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": "/construct-library-sets/IGVFDS6982DESN/"
},
{
"category": "missing sequence specification",
"detail": "Construct library set [IGVFDS6982DESN](/construct-library-sets/IGVFDS6982DESN/) has sequence file(s): [IGVFFI7000JWXA](/sequence-files/IGVFFI7000JWXA/), [IGVFFI5899AJIC](/sequence-files/IGVFFI5899AJIC/), [IGVFFI6383SCZF](/sequence-files/IGVFFI6383SCZF/) 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": "/construct-library-sets/IGVFDS6982DESN/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Construct library set [IGVFDS6982DESN](/construct-library-sets/IGVFDS6982DESN/) 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": "/construct-library-sets/IGVFDS6982DESN/"
}
]
},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization"
},
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6982DESN/",
"accession": "IGVFDS6982DESN",
"file_set_type": "guide library"
}
],
"creation_timestamp": "2023-11-30T22:29:03.831293+00:00",
"demultiplexed_to": [],
"donors": [
"/human-donors/IGVFDO7359LVPI/"
],
"file_sets": [
{
"@id": "/measurement-sets/IGVFDS9665GYVE/",
"accession": "IGVFDS9665GYVE",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinC_AmpliconSequencing"
],
"file_set_type": "experimental data",
"lab": {
"title": "Jesse Engreitz, Stanford"
},
"preferred_assay_title": "Variant FlowFISH",
"status": "released",
"summary": "prime editing Variant FlowFISH integrating a guide (sgRNA) library targeting sequence variants in a genomic locus"
},
{
"@id": "/auxiliary-sets/IGVFDS6148DDTX/",
"accession": "IGVFDS6148DDTX",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep4-BinC_AmpliconSequencing_AuxiliarySet"
],
"file_set_type": "variant sequencing",
"lab": {
"title": "Jesse Engreitz, Stanford"
},
"status": "in progress",
"summary": "variant sequencing for prime editing Variant FlowFISH integrating a guide (sgRNA) library targeting sequence variants in a genomic locus"
},
{
"@id": "/analysis-sets/IGVFDS3423PSID/",
"accession": "IGVFDS3423PSID",
"aliases": [
"jesse-engreitz:PPIF_promoter_tiling_THP1_Variant-FlowFISH_analysis"
],
"file_set_type": "principal analysis",
"lab": {
"title": "Jesse Engreitz, Stanford"
},
"status": "released",
"summary": "prime editing Variant FlowFISH targeting PPIF: variant effects"
}
],
"institutional_certificates": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"cas": "nCas9",
"cas_species": "Streptococcus pyogenes (Sp)",
"fused_domain": "M-MLV RT (PE2)",
"modality": "prime editing",
"status": "released",
"summary": "CRISPR prime editing Sp-nCas9-M-MLV RT (PE2)"
}
],
"multiplexed_in": [],
"notes": "The \"classification\" of this in vitro system was moved into the array property \"classifications.\" This sample's modifications originally included Modification /modifications/e8d549e6-cef0-482a-9deb-76d3b7ecaac3/ which was deleted and replaced with a Crispr Modification igvf:replacement_of_e8d549e6-cef0-482a-9deb-76d3b7ecaac3.",
"origin_of": [],
"parts": [],
"pooled_in": [],
"release_timestamp": "2023-12-20T22:57:29.987372+00:00",
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"term_name": "THP-1"
}
],
"schema_version": "23",
"sex": "male",
"sorted_fractions": [],
"sorted_from": {
"@id": "/in-vitro-systems/IGVFSM1363FPOR/",
"accession": "IGVFSM1363FPOR"
},
"sorted_from_detail": "FACS bin for 51-75% expression of PPIF",
"sources": [
{
"@id": "/sources/atcc/",
"title": "ATCC"
}
],
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"summary": "THP-1 cell line, male, Homo sapiens (sorting details: FACS bin for 51-75% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens",
"uuid": "02dab4f0-6900-4af1-a2d2-ecc4d6fb5ca7",
"virtual": false
}