{
"@context": "/terms/",
"@id": "/in-vitro-systems/IGVFSM4797INCW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4797INCW",
"age": "unknown",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep1-BinA"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Construct library set [IGVFDS4955GEYO](/construct-library-sets/IGVFDS4955GEYO/) has sequence file(s) [IGVFFI5586XFHI](/sequence-files/IGVFFI5586XFHI/), [IGVFFI8337ZCLU](/sequence-files/IGVFFI8337ZCLU/) 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": "/construct-library-sets/IGVFDS4955GEYO/"
},
{
"category": "missing sequence specification",
"detail": "Construct library set [IGVFDS4955GEYO](/construct-library-sets/IGVFDS4955GEYO/) has sequence file(s): [IGVFFI5586XFHI](/sequence-files/IGVFFI5586XFHI/), [IGVFFI8337ZCLU](/sequence-files/IGVFFI8337ZCLU/) 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": "/construct-library-sets/IGVFDS4955GEYO/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing plasmid map",
"detail": "Construct library set [IGVFDS4955GEYO](/construct-library-sets/IGVFDS4955GEYO/) 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/IGVFDS4955GEYO/"
},
{
"category": "missing guide RNA sequences",
"detail": "Construct library set [IGVFDS4955GEYO](/construct-library-sets/IGVFDS4955GEYO/) 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/IGVFDS4955GEYO/"
},
{
"category": "missing analysis",
"detail": "Construct library set [IGVFDS4955GEYO](/construct-library-sets/IGVFDS4955GEYO/) 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": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_input_for",
"path": "/construct-library-sets/IGVFDS4955GEYO/"
}
]
},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization"
},
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS4955GEYO/",
"accession": "IGVFDS4955GEYO",
"file_set_type": "guide library",
"status": "preview"
}
],
"creation_timestamp": "2024-11-25T23:40:40.665432+00:00",
"demultiplexed_to": [],
"donors": [
"/human-donors/IGVFDO7359LVPI/"
],
"file_sets": [
{
"@id": "/measurement-sets/IGVFDS6385NQQG/",
"accession": "IGVFDS6385NQQG",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep1-BinA_AmpliconSequencing"
],
"file_set_type": "experimental data",
"lab": {
"title": "Jesse Engreitz, Stanford"
},
"preferred_assay_title": "Variant-EFFECTS",
"status": "preview",
"summary": "CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus"
},
{
"@id": "/analysis-sets/IGVFDS4833ZRTZ/",
"accession": "IGVFDS4833ZRTZ",
"aliases": [
"jesse-engreitz:PPIF_enhancer_10pegRNA_validation-THP1_Variant-EFFECTS_analysis"
],
"file_set_type": "principal analysis",
"lab": {
"title": "Jesse Engreitz, Stanford"
},
"status": "preview",
"summary": "prime editing Variant-EFFECTS 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": [],
"origin_of": [],
"parts": [],
"pooled_in": [],
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"status": "released",
"term_name": "THP-1"
}
],
"schema_version": "23",
"sex": "male",
"sorted_fractions": [],
"sorted_from": {
"@id": "/in-vitro-systems/IGVFSM3122IKAS/",
"accession": "IGVFSM3122IKAS",
"status": "preview"
},
"sorted_from_detail": "FACS bin for 0-25% expression of PPIF",
"sources": [
{
"@id": "/sources/atcc/",
"status": "released",
"title": "ATCC"
}
],
"status": "preview",
"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 0-25% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens",
"uuid": "c87a08d3-1f50-4314-a3d9-be888edfe77d",
"virtual": false
}