{
"@context": "/terms/",
"@id": "/in-vitro-systems/IGVFSM3948PYPE/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3948PYPE",
"age": "unknown",
"aliases": [
"jesse-engreitz:in-vitro-system_NOS3_CRISPRi_FF_R1_FFrep1_binC_PCR2_S195"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Construct library set [IGVFDS8953DFJK](/construct-library-sets/IGVFDS8953DFJK/) has sequence file(s): [IGVFFI9158VFIB](/sequence-files/IGVFFI9158VFIB/), [IGVFFI7019XQBX](/sequence-files/IGVFFI7019XQBX/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/construct-library-sets/IGVFDS8953DFJK/"
},
{
"category": "NTR term ID",
"detail": "Sample term for [NTR_0000753](/sample-terms/NTR_0000753/) has been newly requested. Ontology terms with a newly requested term ID are expected to have it updated following its addition to the appropriate ontology database.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_ntr_term_id",
"path": "/sample-terms/NTR_0000753/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing analysis",
"detail": "Construct library set [IGVFDS8953DFJK](/construct-library-sets/IGVFDS8953DFJK/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_input_for",
"path": "/construct-library-sets/IGVFDS8953DFJK/"
}
]
},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization"
},
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS8953DFJK/",
"accession": "IGVFDS8953DFJK",
"file_set_type": "guide library",
"status": "released"
}
],
"creation_timestamp": "2024-04-15T19:53:19.765161+00:00",
"demultiplexed_to": [],
"donors": [
"/human-donors/IGVFDO3459DFTW/"
],
"file_sets": [
{
"@id": "/auxiliary-sets/IGVFDS7773OUJT/",
"accession": "IGVFDS7773OUJT",
"aliases": [
"jesse-engreitz:auxiliary_NOS3_CRISPRi_FF_R1_FFrep1_binC_PCR2_S195"
],
"file_set_type": "gRNA sequencing",
"lab": {
"title": "Jesse Engreitz, Stanford"
},
"status": "released",
"summary": "gRNA sequencing for CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting sequence variants, transcription start sites in NOS3"
},
{
"@id": "/measurement-sets/IGVFDS5321JEBO/",
"accession": "IGVFDS5321JEBO",
"aliases": [
"jesse-engreitz:measurement_NOS3_CRISPRi_FF_R1_FFrep1_binC_PCR2_S195"
],
"file_set_type": "experimental data",
"lab": {
"title": "Jesse Engreitz, Stanford"
},
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released",
"summary": "CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting sequence variants, transcription start sites in NOS3"
},
{
"@id": "/analysis-sets/IGVFDS7917YHKA/",
"accession": "IGVFDS7917YHKA",
"aliases": [
"jesse-engreitz:analysis_set_NOS3_CRISPRI-FF"
],
"file_set_type": "principal analysis",
"lab": {
"title": "Jesse Engreitz, Stanford"
},
"status": "in progress",
"summary": "CRISPR interference FlowFISH screen targeting NOS3"
}
],
"institutional_certificates": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"modifications": [
{
"@id": "/crispr-modifications/b4bc725a-8eeb-4180-9789-bece3516c0c1/",
"cas": "dCas9",
"cas_species": "Streptococcus pyogenes (Sp)",
"fused_domain": "KOX1-KRAB",
"modality": "interference",
"status": "released",
"summary": "CRISPRi Sp-dCas9-KOX1-KRAB"
}
],
"multiplexed_in": [],
"notes": "This sample's modifications originally included Modification /modifications/2ba01755-df67-453b-b047-f7cdba236665/ which was deleted and replaced with a Crispr Modification igvf:replacement_of_2ba01755-df67-453b-b047-f7cdba236665.",
"origin_of": [],
"parts": [],
"pooled_in": [],
"release_timestamp": "2024-06-22T00:20:42.900698+00:00",
"sample_terms": [
{
"@id": "/sample-terms/NTR_0000753/",
"status": "released",
"term_name": "TeloHAEC"
}
],
"schema_version": "23",
"sex": "female",
"sorted_fractions": [],
"sorted_from": {
"@id": "/in-vitro-systems/IGVFSM0897QVAK/",
"accession": "IGVFSM0897QVAK",
"status": "released"
},
"sorted_from_detail": "FACS bin C for 51-75% expression of NOS3",
"sources": [
{
"@id": "/sources/atcc/",
"status": "released",
"title": "ATCC"
}
],
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"summary": "TeloHAEC cell line, female, Homo sapiens (sorting details: FACS bin C for 51-75% expression of NOS3) modified with CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"taxa": "Homo sapiens",
"uuid": "a86d9dda-a45d-49f8-8ed7-47e6eee4f4ec",
"virtual": false
}