{
"@context": "/terms/",
"@id": "/in-vitro-systems/IGVFSM9542NUGS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9542NUGS",
"age": "unknown",
"aliases": [
"jay-shendure:CRISPRa_VPR_K562_10Xlane2"
],
"audit": {
"WARNING": [
{
"category": "missing files",
"detail": "Construct library set [IGVFDS7581DNXF](/construct-library-sets/IGVFDS7581DNXF/) has no `files`. File sets are expected to have files.",
"level": 40,
"level_name": "WARNING",
"name": "audit_no_files",
"path": "/construct-library-sets/IGVFDS7581DNXF/"
}
]
},
"award": {
"@id": "/awards/HG011966/",
"component": "functional characterization"
},
"cellular_sub_pool": "10Xlane2",
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS7581DNXF/",
"accession": "IGVFDS7581DNXF",
"file_set_type": "guide library",
"status": "released"
}
],
"creation_timestamp": "2023-12-01T23:56:02.982233+00:00",
"demultiplexed_to": [],
"donors": [
"/human-donors/IGVFDO9208RPQQ/"
],
"file_sets": [
{
"@id": "/auxiliary-sets/IGVFDS4834SKZS/",
"accession": "IGVFDS4834SKZS",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VPR_10Xlane2_CS1"
],
"file_set_type": "gRNA sequencing",
"lab": {
"title": "Jay Shendure, UW"
},
"status": "released",
"summary": "gRNA sequencing for scCRISPR activation screen integrating a guide (sgRNA) library targeting TF binding sites, candidate cis-regulatory elements in many genomic loci"
},
{
"@id": "/measurement-sets/IGVFDS0508ERUQ/",
"accession": "IGVFDS0508ERUQ",
"aliases": [
"jay-shendure:CRISPRa_singlecell_K562_VPR_10Xlane2_exprs"
],
"file_set_type": "experimental data",
"lab": {
"title": "Jay Shendure, UW"
},
"preferred_assay_title": "scCRISPR screen",
"status": "released",
"summary": "scCRISPR activation screen integrating a guide (sgRNA) library targeting TF binding sites, candidate cis-regulatory elements in many genomic loci"
},
{
"@id": "/analysis-sets/IGVFDS9078ZWQH/",
"accession": "IGVFDS9078ZWQH",
"aliases": [
"jay-shendure:analysis_set_CRISPRa_K562"
],
"file_set_type": "principal analysis",
"lab": {
"title": "Jay Shendure, UW"
},
"status": "released",
"summary": "scCRISPR activation screen: differential gene expression quantifications, sparse gene count matrix"
}
],
"institutional_certificates": [],
"lab": {
"@id": "/labs/jay-shendure/",
"title": "Jay Shendure, UW"
},
"modifications": [
{
"@id": "/crispr-modifications/8b61bce4-105c-435e-9b32-1c8903566a9b/",
"cas": "dCas9",
"cas_species": "Streptococcus pyogenes (Sp)",
"fused_domain": "VP64-p65-Rta (VPR)",
"modality": "activation",
"status": "released",
"summary": "CRISPRa Sp-dCas9-VP64-p65-Rta (VPR)"
}
],
"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/ec803a15-a3c1-4d14-b1be-be3a5ea1ef8a/ which was deleted and replaced with a Crispr Modification igvf:replacement_of_ec803a15-a3c1-4d14-b1be-be3a5ea1ef8a.",
"origin_of": [],
"part_of": "/in-vitro-systems/IGVFSM8338YZLA/",
"parts": [],
"pooled_in": [],
"product_id": "HD_dCas9-VPR-005",
"publications": [
{
"@id": "/publications/20fcbdbb-5a47-41c6-b80b-e6dd0e8a8d3e/",
"publication_identifiers": [
"doi:10.1101/2023.03.28.534017",
"doi:10.1038/s41467-024-52490-4"
],
"status": "released"
}
],
"release_timestamp": "2024-08-13T20:47:08.064750+00:00",
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002067/",
"status": "released",
"term_name": "K562"
}
],
"schema_version": "23",
"sex": "female",
"sorted_fractions": [],
"sources": [
{
"@id": "/sources/horizondiscovery/",
"status": "released",
"title": "Horizon"
}
],
"status": "released",
"submitted_by": {
"@id": "/users/73f58e9f-8f5d-4fee-a7cd-dd63c0167e4b/",
"title": "Beth Martin"
},
"summary": "K562 cell line (cellular sub pool: 10Xlane2), female, Homo sapiens modified with CRISPRa Sp-dCas9-VP64-p65-Rta (VPR), transfected with a guide library",
"taxa": "Homo sapiens",
"url": "https://horizondiscovery.com/en/engineered-cell-lines/products/dcas9-vpr-stable-cell-line",
"uuid": "bfc50287-e72f-4fc9-80eb-a8d0641cbe5e",
"virtual": false
}