{
"@context": "/terms/",
"@id": "/in-vitro-systems/IGVFSM1063UQVF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1063UQVF",
"age": "unknown",
"aliases": [
"gary-hon:differentiated_H9_shen_construct_sgRNA_PB_LW273"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Preview construct library set [IGVFDS9629YZLO](/construct-library-sets/IGVFDS9629YZLO/) has in progress subobject tabular file [IGVFFI4543YHDW](/tabular-files/IGVFFI4543YHDW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/construct-library-sets/IGVFDS9629YZLO/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing plasmid map",
"detail": "Construct library set [IGVFDS9629YZLO](/construct-library-sets/IGVFDS9629YZLO/) 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/IGVFDS9629YZLO/"
}
],
"WARNING": [
{
"category": "missing files",
"detail": "Construct library set [IGVFDS9629YZLO](/construct-library-sets/IGVFDS9629YZLO/) has no `files`. File sets are expected to have files.",
"level": 40,
"level_name": "WARNING",
"name": "audit_no_files",
"path": "/construct-library-sets/IGVFDS9629YZLO/"
}
]
},
"award": {
"@id": "/awards/HG011996/",
"component": "functional characterization"
},
"cell_fate_change_protocol": "/documents/3959d1b4-07fd-4841-864a-c2e7b4381edb/",
"cellular_sub_pool": "subpool_LW273",
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS9629YZLO/",
"accession": "IGVFDS9629YZLO",
"file_set_type": "guide library",
"status": "preview"
}
],
"creation_timestamp": "2024-04-25T21:26:52.055556+00:00",
"demultiplexed_to": [],
"documents": [
"/documents/3959d1b4-07fd-4841-864a-c2e7b4381edb/"
],
"donors": [
"/human-donors/IGVFDO2718IDDQ/"
],
"file_sets": [
{
"@id": "/auxiliary-sets/IGVFDS7977FNRB/",
"accession": "IGVFDS7977FNRB",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_HTO_PB_LW273"
],
"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": "/auxiliary-sets/IGVFDS5841QQSW/",
"accession": "IGVFDS5841QQSW",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_sgRNA_PB_LW273"
],
"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": "/measurement-sets/IGVFDS1050IJPU/",
"accession": "IGVFDS1050IJPU",
"aliases": [
"gary-hon:CM_Pilot_2_Mini_PB_LW273"
],
"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/IGVFDS4762GRIW/",
"accession": "IGVFDS4762GRIW",
"aliases": [
"gary-hon:H9_shen_construct_sgRNA_PB_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"
}
],
"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": "transfection",
"origin_of": [],
"originated_from": {
"@id": "/in-vitro-systems/IGVFSM3927QOQT/",
"accession": "IGVFSM3927QOQT",
"status": "preview"
},
"part_of": "/in-vitro-systems/IGVFSM1649MDAH/",
"parts": [],
"pooled_in": [],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0003045/",
"status": "released",
"term_name": "H9"
}
],
"schema_version": "23",
"sex": "female",
"sorted_fractions": [],
"sources": [
{
"@id": "/labs/gary-hon/",
"status": "current",
"title": "Gary Hon, UT"
}
],
"status": "preview",
"submitted_by": {
"@id": "/users/b05645f1-2d56-4a5e-b272-4601e555a3fa/",
"title": "Mpathi Nzima"
},
"summary": "H9 differentiated cell specimen induced to cardiac muscle cell for 12 days (cellular sub pool: subpool_LW273), female, Homo sapiens modified with CRISPRi Sp-dCas9, transfected 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": "018b84a4-1b82-40a2-a6f2-dac38a448e9e",
"virtual": false
}