{
"@context": "/terms/",
"@id": "/in-vitro-systems/IGVFSM8286CXGJ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8286CXGJ",
"age": "unknown",
"aliases": [
"daniel-bauer:ChrX_Screen_ABE8e_day14_rep2_ivs"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Construct library set [IGVFDS7616NEZY](/construct-library-sets/IGVFDS7616NEZY/) has sequence file(s): [IGVFFI0981NEKU](/sequence-files/IGVFFI0981NEKU/), [IGVFFI7232DMOC](/sequence-files/IGVFFI7232DMOC/), [IGVFFI7009DYJJ](/sequence-files/IGVFFI7009DYJJ/), [IGVFFI3043KBWQ](/sequence-files/IGVFFI3043KBWQ/), [IGVFFI2830SKUX](/sequence-files/IGVFFI2830SKUX/), [IGVFFI9174EBBV](/sequence-files/IGVFFI9174EBBV/) which do not have any `seqspecs`. Sequence files in a file set associated with bulk data are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/construct-library-sets/IGVFDS7616NEZY/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM8286CXGJ](/in-vitro-systems/IGVFSM8286CXGJ/) has in progress subobject construct library set [IGVFDS7616NEZY](/construct-library-sets/IGVFDS7616NEZY/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM8286CXGJ/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM8286CXGJ](/in-vitro-systems/IGVFSM8286CXGJ/) has in progress subobject crispr modification [df6a701e-a9f4-4908-a5fd-8d6687c2694d](/crispr-modifications/df6a701e-a9f4-4908-a5fd-8d6687c2694d/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM8286CXGJ/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing associated phenotypes",
"detail": "Construct library set [IGVFDS7616NEZY](/construct-library-sets/IGVFDS7616NEZY/) has phenotype-associated variants listed in its `selection_criteria`, but no phenotype term specified in `associated_phenotypes`. Construct library sets with a selection criteria of phenotype-associated variants are expected to have associated phenotype(s).",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_construct_library_set_associated_phenotypes",
"path": "/construct-library-sets/IGVFDS7616NEZY/"
},
{
"category": "missing plasmid map",
"detail": "Construct library set [IGVFDS7616NEZY](/construct-library-sets/IGVFDS7616NEZY/) 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/IGVFDS7616NEZY/"
}
]
},
"award": {
"@id": "/awards/HG012010/",
"component": "functional characterization"
},
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS7616NEZY/",
"accession": "IGVFDS7616NEZY",
"file_set_type": "guide library",
"status": "in progress"
}
],
"creation_timestamp": "2024-09-10T17:28:40.386217+00:00",
"demultiplexed_to": [],
"description": "14 days after transfection with lentiviral sgRNA library",
"donors": [
{
"@id": "/human-donors/IGVFDO0965QSBA/",
"accession": "IGVFDO0965QSBA",
"ethnicities": [
"Japanese"
],
"status": "released"
}
],
"file_sets": [
{
"@id": "/measurement-sets/IGVFDS5228ZNHR/",
"accession": "IGVFDS5228ZNHR",
"aliases": [
"daniel-bauer:ChrX_Screen_ABE8e_day14_rep2_ms"
],
"file_set_type": "experimental data",
"lab": {
"title": "Daniel Bauer, HSCI"
},
"preferred_assay_title": "Proliferation CRISPR screen",
"status": "released",
"summary": "Proliferation CRISPR base editing screen integrating a guide (sgRNA) library targeting phenotype-associated variants genome-wide"
},
{
"@id": "/analysis-sets/IGVFDS0120EBCZ/",
"accession": "IGVFDS0120EBCZ",
"aliases": [
"daniel-bauer:chrX_mageck_analysis_set"
],
"file_set_type": "principal analysis",
"lab": {
"title": "Daniel Bauer, HSCI"
},
"status": "released",
"summary": "Proliferation CRISPR base editing, cutting screen: guide quantifications, variant effects"
}
],
"institutional_certificates": [],
"lab": {
"@id": "/labs/daniel-bauer/",
"title": "Daniel Bauer, HSCI"
},
"modifications": [
{
"@id": "/crispr-modifications/df6a701e-a9f4-4908-a5fd-8d6687c2694d/",
"cas": "SpRY",
"cas_species": "Streptococcus pyogenes (Sp)",
"fused_domain": "ABE8e",
"modality": "base editing",
"status": "in progress",
"summary": "CRISPR base editing SpRY-ABE8e"
}
],
"multiplexed_in": [],
"nucleic_acid_delivery": "lentiviral transduction",
"origin_of": [],
"parts": [],
"pooled_in": [],
"release_timestamp": "2025-03-07T23:01:33.239557+00:00",
"sample_terms": [
{
"@id": "/sample-terms/EFO_0022838/",
"status": "released",
"term_name": "HUDEP-2"
}
],
"schema_version": "25",
"sex": "unspecified",
"sorted_fractions": [],
"sources": [
{
"@id": "/labs/daniel-bauer/",
"status": "current",
"title": "Daniel Bauer, HSCI"
}
],
"status": "released",
"submitted_by": {
"@id": "/users/96fd4846-bfa6-47db-ac12-495df29943ee/",
"title": "Eric Che"
},
"summary": "HUDEP-2 cell line, Homo sapiens modified with CRISPR base editing SpRY-ABE8e, transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens",
"time_post_library_delivery": 14,
"time_post_library_delivery_units": "day",
"uuid": "e1d18b01-f9d1-4bd5-9ad5-3a20c3581386",
"virtual": false
}