{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0884TWTU/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0884TWTU",
"aliases": [
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR1-Rep1_S5",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR2-Rep1_S11",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR3-Rep1_S59",
"jesse-engreitz:measurement_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR4-Rep1_S65"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8183BLZH](/auxiliary-sets/IGVFDS8183BLZH/) has sequence file(s) [IGVFFI2821MABS](/sequence-files/IGVFFI2821MABS/), [IGVFFI5991CNOJ](/sequence-files/IGVFFI5991CNOJ/), [IGVFFI6907NDCS](/sequence-files/IGVFFI6907NDCS/), [IGVFFI3035ARRF](/sequence-files/IGVFFI3035ARRF/) 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": "/auxiliary-sets/IGVFDS8183BLZH/"
}
],
"WARNING": [
{
"category": "missing files",
"detail": "Measurement set [IGVFDS0884TWTU](/measurement-sets/IGVFDS0884TWTU/) has no `files`. File sets are expected to have files.",
"level": 40,
"level_name": "WARNING",
"name": "audit_no_files",
"path": "/measurement-sets/IGVFDS0884TWTU/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8183BLZH/",
"accession": "IGVFDS8183BLZH",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR1-Rep1_S5",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR2-Rep1_S11",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR3-Rep1_S59",
"jesse-engreitz:auxiliary_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR4-Rep1_S65"
],
"file_set_type": "gRNA sequencing",
"status": "released"
},
{
"@id": "/auxiliary-sets/IGVFDS1546MEZJ/",
"accession": "IGVFDS1546MEZJ",
"aliases": [
"jesse-engreitz:auxiliary_sortparams_CRUDO_SSFA2-Auxin0hrs-FF1"
],
"file_set_type": "cell sorting",
"status": "released"
}
],
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
"control_for": [],
"creation_timestamp": "2024-05-14T20:32:55.202590+00:00",
"documents": [
"/documents/74d53b9c-ab1d-42e3-b679-d3a00ae3d842/"
],
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"accession": "IGVFDO0384OZRW",
"aliases": [
"igvf:donor_of_HCT116"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [],
"input_for": [
"/analysis-sets/IGVFDS2031CTSP/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set.",
"preferred_assay_title": "CRISPR FlowFISH screen",
"protocols": [
"https://www.protocols.io/view/crispri-of-regulatory-elements-upon-degron-operati-5jyl82d59l2w/v1"
],
"release_timestamp": "2024-07-10T19:51:11.991417+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7435FSSP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7435FSSP",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR1-Rep1_S5",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR2-Rep1_S11",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR3-Rep1_S59",
"jesse-engreitz:in-vitro-system_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR4-Rep1_S65"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS5413RKIA/",
"accession": "IGVFDS5413RKIA",
"file_set_type": "guide library",
"status": "released",
"summary": "guide (sgRNA) library targeting accessible genome regions in many genomic loci"
}
],
"modifications": [
{
"@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
"modality": "interference",
"status": "released"
},
{
"@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
"modality": "degradation",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002824/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:HCT116"
],
"status": "released",
"summary": "HCT116",
"term_name": "HCT116"
}
],
"status": "released",
"summary": "HCT116 cell line, male, Homo sapiens (sorting details: FACS bin E for 80-90% expression of SSFA2) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"submitted_files_timestamp": "2024-06-01T01:44:47.399156+00:00",
"summary": "mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci",
"targeted_genes": [
{
"@id": "/genes/ENSG00000138434/",
"geneid": "ENSG00000138434",
"name": "ITPR interacting domain containing 2",
"status": "released",
"symbol": "ITPRID2",
"synonyms": [
"sperm specific antigen 2",
"KRAP",
"sperm associated antigen 13",
"SSFA2",
"ki-ras-induced actin-interacting protein",
"SPAG13",
"ITPR-interacting domain-containing protein 2",
"CS-1",
"CS1",
"protein ITPRID2",
"KRAS-induced actin-interacting protein",
"cleavage signal-1 protein"
]
}
],
"uuid": "285870c4-091b-4d2c-a6ac-9fb9fb59a9ca"
}