{
"@context": "/terms/",
"@id": "/in-vitro-systems/IGVFSM9103RFFD/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9103RFFD",
"age": "unknown",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinD"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Construct library set [IGVFDS6128KVUP](/construct-library-sets/IGVFDS6128KVUP/) has sequence file(s) [IGVFFI3027JYLB](/sequence-files/IGVFFI3027JYLB/), [IGVFFI3514ALUV](/sequence-files/IGVFFI3514ALUV/), [IGVFFI2649OSZF](/sequence-files/IGVFFI2649OSZF/) 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/IGVFDS6128KVUP/"
},
{
"category": "missing sequence specification",
"detail": "Construct library set [IGVFDS6128KVUP](/construct-library-sets/IGVFDS6128KVUP/) has sequence file(s): [IGVFFI3027JYLB](/sequence-files/IGVFFI3027JYLB/), [IGVFFI3514ALUV](/sequence-files/IGVFFI3514ALUV/), [IGVFFI2649OSZF](/sequence-files/IGVFFI2649OSZF/) 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/IGVFDS6128KVUP/"
},
{
"category": "mismatched status",
"detail": "Preview in vitro system [IGVFSM9103RFFD](/in-vitro-systems/IGVFSM9103RFFD/) has in progress subobject treatment [cf87f410-54ee-48ef-b654-8443c4fee032](/treatments/cf87f410-54ee-48ef-b654-8443c4fee032/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM9103RFFD/"
},
{
"category": "mismatched status",
"detail": "Preview in vitro system [IGVFSM9103RFFD](/in-vitro-systems/IGVFSM9103RFFD/) has in progress subobject treatment [4b5f0d13-ec20-4b91-85f5-a009cd91451f](/treatments/4b5f0d13-ec20-4b91-85f5-a009cd91451f/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM9103RFFD/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing plasmid map",
"detail": "Construct library set [IGVFDS6128KVUP](/construct-library-sets/IGVFDS6128KVUP/) 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/IGVFDS6128KVUP/"
},
{
"category": "missing guide RNA sequences",
"detail": "Construct library set [IGVFDS6128KVUP](/construct-library-sets/IGVFDS6128KVUP/) 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/IGVFDS6128KVUP/"
},
{
"category": "missing analysis",
"detail": "Construct library set [IGVFDS6128KVUP](/construct-library-sets/IGVFDS6128KVUP/) 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/IGVFDS6128KVUP/"
}
]
},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization"
},
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6128KVUP/",
"accession": "IGVFDS6128KVUP",
"file_set_type": "guide library",
"status": "preview"
}
],
"creation_timestamp": "2024-11-21T21:52:50.593110+00:00",
"demultiplexed_to": [],
"donors": [
"/human-donors/IGVFDO1080XFGV/"
],
"file_sets": [
{
"@id": "/measurement-sets/IGVFDS0414OFOP/",
"accession": "IGVFDS0414OFOP",
"aliases": [
"jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep1-BinD_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/IGVFDS1824XDMU/",
"accession": "IGVFDS1824XDMU",
"aliases": [
"jesse-engreitz:IL2RA_promoter_tiling_Jurkat-Stimulation_Variant-EFFECTS_analysis"
],
"file_set_type": "principal analysis",
"lab": {
"title": "Jesse Engreitz, Stanford"
},
"status": "preview",
"summary": "prime editing Variant-EFFECTS targeting IL2RA: 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_0002796/",
"status": "released",
"term_name": "Jurkat"
}
],
"schema_version": "23",
"sex": "male",
"sorted_fractions": [],
"sorted_from": {
"@id": "/in-vitro-systems/IGVFSM1981RVAJ/",
"accession": "IGVFSM1981RVAJ",
"status": "preview"
},
"sorted_from_detail": "FACS bin for 76-100% expression of IL2RA",
"sources": [
{
"@id": "/sources/atcc/",
"status": "released",
"title": "ATCC"
}
],
"status": "preview",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"summary": "Jurkat cell line, male, Homo sapiens (sorting details: FACS bin for 76-100% expression of IL2RA) treated with 100 ng/mL phorbol 13-acetate 12-myristate for 24 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 24 hours, modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/4b5f0d13-ec20-4b91-85f5-a009cd91451f/",
"depletion": false,
"purpose": "stimulation",
"status": "in progress",
"treatment_term_name": "phorbol 13-acetate 12-myristate",
"treatment_type": "chemical"
},
{
"@id": "/treatments/cf87f410-54ee-48ef-b654-8443c4fee032/",
"depletion": false,
"purpose": "stimulation",
"status": "in progress",
"treatment_term_name": "T-cell surface glycoprotein CD3 gamma chain",
"treatment_type": "protein"
}
],
"uuid": "a1952654-521e-4bfb-959f-d6fcea934897",
"virtual": false
}