{
"@context": "/terms/",
"@id": "/in-vitro-systems/IGVFSM9913PXTT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9913PXTT",
"age": "unknown",
"aliases": [
"jay-shendure:CRISPRa_VPH_NGN2_WTC11_neurons_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"
},
"cell_fate_change_protocol": "/documents/a9ab6aae-48a0-444a-a609-3addf65d3027/",
"cellular_sub_pool": "10Xlane2",
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS7581DNXF/",
"accession": "IGVFDS7581DNXF",
"file_set_type": "guide library"
}
],
"creation_timestamp": "2023-12-01T23:56:06.526253+00:00",
"demultiplexed_to": [],
"donors": [
"/human-donors/IGVFDO1756PPKO/"
],
"file_sets": [
{
"@id": "/auxiliary-sets/IGVFDS2220HHTN/",
"accession": "IGVFDS2220HHTN",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_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/IGVFDS0272VVTX/",
"accession": "IGVFDS0272VVTX",
"aliases": [
"jay-shendure:CRISPRa_singlecell_iPSC-derived-neurons_VPH_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/IGVFDS4021XJLW/",
"accession": "IGVFDS4021XJLW",
"aliases": [
"jay-shendure:analysis_set_CRISPRa_ipscNeurons"
],
"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/426a4099-35d9-4c65-8851-5e788a3d4e70/",
"cas": "dCas9",
"cas_species": "Streptococcus pyogenes (Sp)",
"fused_domain": "VPH",
"modality": "activation",
"status": "released",
"summary": "CRISPRa Sp-dCas9-VPH"
}
],
"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/2ca03166-1fc8-49fd-a4f9-42184b949ae5/ which was deleted and replaced with a Crispr Modification igvf:replacement_of_2ca03166-1fc8-49fd-a4f9-42184b949ae5.",
"origin_of": [],
"part_of": "/in-vitro-systems/IGVFSM9003EMOQ/",
"parts": [],
"pooled_in": [],
"publications": [
{
"@id": "/publications/20fcbdbb-5a47-41c6-b80b-e6dd0e8a8d3e/",
"publication_identifiers": [
"doi:10.1101/2023.03.28.534017"
]
}
],
"release_timestamp": "2024-08-13T20:47:21.526289+00:00",
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"term_name": "GM25256 (WTC-11)"
}
],
"schema_version": "23",
"sex": "male",
"sorted_fractions": [],
"sources": [
{
"@id": "/sources/martin-kampmann/",
"title": "Martin Kampmann, UCSF"
}
],
"status": "released",
"submitted_by": {
"@id": "/users/73f58e9f-8f5d-4fee-a7cd-dd63c0167e4b/",
"title": "Beth Martin"
},
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to neuron for 19 days (cellular sub pool: 10Xlane2), male, Homo sapiens modified with CRISPRa Sp-dCas9-VPH, transfected with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000540/",
"term_name": "neuron"
},
"taxa": "Homo sapiens",
"time_post_change": 19,
"time_post_change_units": "day",
"uuid": "b4cd7711-690d-4b36-9fd5-665722969a54",
"virtual": false
}