{
"@context": "/terms/",
"@id": "/in-vitro-systems/IGVFSM6928JPHO/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6928JPHO",
"age": "unknown",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR1-Rep1_S136",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR2-Rep1_S142",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR3-Rep1_S190",
"jesse-engreitz:in-vitro-system_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR4-Rep1_S196"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Construct library set [IGVFDS1891GTLU](/construct-library-sets/IGVFDS1891GTLU/) has sequence file(s) [IGVFFI0445AYJF](/sequence-files/IGVFFI0445AYJF/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/construct-library-sets/IGVFDS1891GTLU/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing analysis",
"detail": "Construct library set [IGVFDS1891GTLU](/construct-library-sets/IGVFDS1891GTLU/) 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/IGVFDS1891GTLU/"
}
]
},
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization"
},
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS1891GTLU/",
"accession": "IGVFDS1891GTLU",
"file_set_type": "guide library",
"status": "released"
}
],
"creation_timestamp": "2024-05-09T23:20:53.200377+00:00",
"demultiplexed_to": [],
"documents": [
"/documents/a1a19741-90cc-46ea-b90c-96c4a4b70d8e/",
"/documents/b0663905-6249-42ea-9937-9b2f645c787d/"
],
"donors": [
"/human-donors/IGVFDO0384OZRW/"
],
"file_sets": [
{
"@id": "/measurement-sets/IGVFDS2315UDUR/",
"accession": "IGVFDS2315UDUR",
"aliases": [
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR1-Rep1_S136",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR2-Rep1_S142",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR3-Rep1_S190",
"jesse-engreitz:measurement_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR4-Rep1_S196"
],
"file_set_type": "experimental data",
"lab": {
"title": "Jesse Engreitz, Stanford"
},
"preferred_assay_title": "CRISPR FlowFISH screen",
"status": "released",
"summary": "mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci"
},
{
"@id": "/auxiliary-sets/IGVFDS9525OEUV/",
"accession": "IGVFDS9525OEUV",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR1-Rep1_S136",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR2-Rep1_S142",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR3-Rep1_S190",
"jesse-engreitz:auxiliary_CRUDO_FAM3C_Auxin6hrs-FF1-BinD-PCR4-Rep1_S196"
],
"file_set_type": "gRNA sequencing",
"lab": {
"title": "Jesse Engreitz, Stanford"
},
"status": "released",
"summary": "gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci"
},
{
"@id": "/auxiliary-sets/IGVFDS9190KTAF/",
"accession": "IGVFDS9190KTAF",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_FAM3C_Auxin6hrs-FF1"
],
"file_set_type": "cell sorting",
"lab": {
"title": "Jesse Engreitz, Stanford"
},
"status": "released",
"summary": "cell sorting for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci, mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci, ... and 4 more measurement sets"
},
{
"@id": "/analysis-sets/IGVFDS5239VQTN/",
"accession": "IGVFDS5239VQTN",
"aliases": [
"jesse-engreitz:analysis_set_CRUDO_FAM3C"
],
"file_set_type": "principal analysis",
"lab": {
"title": "Jesse Engreitz, Stanford"
},
"status": "in progress",
"summary": "CRISPR degradation, interference FlowFISH screen targeting FAM3C: differential element quantifications"
}
],
"institutional_certificates": [],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"modifications": [
{
"@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
"degron_system": "AID",
"modality": "degradation",
"status": "released",
"summary": "AID system targeting RAD21",
"tagged_proteins": [
{
"@id": "/genes/ENSG00000164754/",
"status": "released",
"summary": "RAD21 - ENSG00000164754 (Homo sapiens)",
"symbol": "RAD21"
}
]
},
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"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/56d6a4f4-5fa4-4989-890e-aafb032f1e7d/ which was deleted and replaced with a Crispr Modification igvf:replacement_of_56d6a4f4-5fa4-4989-890e-aafb032f1e7d.",
"origin_of": [],
"parts": [],
"pooled_in": [],
"release_timestamp": "2024-07-10T19:41:05.421396+00:00",
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"status": "released",
"term_name": "HCT116"
}
],
"schema_version": "23",
"sex": "male",
"sorted_fractions": [],
"sorted_from": {
"@id": "/in-vitro-systems/IGVFSM4608EHIU/",
"accession": "IGVFSM4608EHIU",
"status": "released"
},
"sorted_from_detail": "FACS bin D for 55-65% expression of FAM3C",
"sources": [
{
"@id": "/sources/atcc/",
"status": "released",
"title": "ATCC"
}
],
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin D for 55-65% expression of FAM3C) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
"depletion": false,
"purpose": "activation",
"status": "released",
"treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid",
"treatment_type": "chemical"
}
],
"uuid": "eb41e091-7a54-4f79-9894-d2b16213de01",
"virtual": false
}