{
"@context": "/terms/",
"@id": "/in-vitro-systems/IGVFSM0559UNMK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0559UNMK",
"age": "unknown",
"aliases": [
"nikhil-munshi:differentited_WTC11_TF_Perturb_Seq_Pilot_CMs_Lenti_LW279"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Preview construct library set [IGVFDS2302LCEO](/construct-library-sets/IGVFDS2302LCEO/) has in progress subobject tabular file [IGVFFI7568FEHI](/tabular-files/IGVFFI7568FEHI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/construct-library-sets/IGVFDS2302LCEO/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing plasmid map",
"detail": "Construct library set [IGVFDS2302LCEO](/construct-library-sets/IGVFDS2302LCEO/) 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/IGVFDS2302LCEO/"
}
],
"WARNING": [
{
"category": "missing files",
"detail": "Construct library set [IGVFDS2302LCEO](/construct-library-sets/IGVFDS2302LCEO/) has no `files`. File sets are expected to have files.",
"level": 40,
"level_name": "WARNING",
"name": "audit_no_files",
"path": "/construct-library-sets/IGVFDS2302LCEO/"
}
]
},
"award": {
"@id": "/awards/HG011996/",
"component": "functional characterization"
},
"cell_fate_change_protocol": "/documents/3959d1b4-07fd-4841-864a-c2e7b4381edb/",
"cellular_sub_pool": "subpool_LW279",
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2302LCEO/",
"accession": "IGVFDS2302LCEO",
"file_set_type": "guide library",
"status": "preview"
}
],
"creation_timestamp": "2024-03-13T19:49:21.308691+00:00",
"demultiplexed_to": [],
"description": "differentiated WTC11 -dCAS9-KRAB-Lenti-sgRNA",
"documents": [
"/documents/3959d1b4-07fd-4841-864a-c2e7b4381edb/"
],
"donors": [
"/human-donors/IGVFDO1756PPKO/"
],
"file_sets": [
{
"@id": "/auxiliary-sets/IGVFDS0997MTQA/",
"accession": "IGVFDS0997MTQA",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_sgRNA_LW279"
],
"file_set_type": "gRNA sequencing",
"lab": {
"title": "Gary Hon, UT"
},
"status": "preview",
"summary": "gRNA sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci"
},
{
"@id": "/auxiliary-sets/IGVFDS7027VRZT/",
"accession": "IGVFDS7027VRZT",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_HTO_LW279"
],
"file_set_type": "cell hashing barcode sequencing",
"lab": {
"title": "Gary Hon, UT"
},
"status": "preview",
"summary": "cell hashing barcode sequencing for CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci"
},
{
"@id": "/measurement-sets/IGVFDS7733OTCA/",
"accession": "IGVFDS7733OTCA",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_LW279"
],
"file_set_type": "experimental data",
"lab": {
"title": "Gary Hon, UT"
},
"preferred_assay_title": "Perturb-seq",
"status": "preview",
"summary": "CRISPR interference Perturb-seq integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci"
},
{
"@id": "/analysis-sets/IGVFDS4389OUWU/",
"accession": "IGVFDS4389OUWU",
"aliases": [
"gary-hon:TF_Perturb_Seq_Pilot_Lenti_CM_PrimaryAnalysis"
],
"file_set_type": "principal analysis",
"lab": {
"title": "Gary Hon, UT"
},
"status": "preview",
"summary": "interference Perturb-seq: filtered feature barcode matrix, raw feature barcode matrix, sparse gene count matrix, unfiltered global differential expression, unfiltered local differential expression"
}
],
"institutional_certificates": [],
"lab": {
"@id": "/labs/gary-hon/",
"title": "Gary Hon, UT"
},
"modifications": [
{
"@id": "/crispr-modifications/0a63b754-eca4-44aa-bbc2-fccdc6c44fb5/",
"cas": "dCas9",
"cas_species": "Streptococcus pyogenes (Sp)",
"modality": "interference",
"status": "preview",
"summary": "CRISPRi Sp-dCas9"
}
],
"multiplexed_in": [],
"notes": "This sample's modifications originally included Modification /modifications/5f12e117-5d61-464b-a1e5-c826c83d6b10/ which was deleted and replaced with a Crispr Modification igvf:replacement_of_5f12e117-5d61-464b-a1e5-c826c83d6b10.",
"nucleic_acid_delivery": "lentiviral transduction",
"origin_of": [],
"originated_from": {
"@id": "/in-vitro-systems/IGVFSM6456YEWR/",
"accession": "IGVFSM6456YEWR",
"status": "preview"
},
"part_of": "/in-vitro-systems/IGVFSM6351SIZQ/",
"parts": [],
"pooled_in": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"status": "released",
"term_name": "GM25256 (WTC-11)"
}
],
"schema_version": "23",
"sex": "male",
"sorted_fractions": [],
"sources": [
{
"@id": "/labs/nikhil-munshi/",
"status": "current",
"title": "Nikhil Munshi, UT"
}
],
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"submitter_comment": "DIfferentiated WTC11 cell line (Lenti)",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW279), male, Homo sapiens modified with CRISPRi Sp-dCas9, transduced (lentivirus) with a guide library",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens",
"time_post_change": 12,
"time_post_change_units": "day",
"time_post_library_delivery": 3,
"time_post_library_delivery_units": "week",
"uuid": "cf1353b0-3b4d-41a2-81e0-f816a7d1d936",
"virtual": false
}