{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS9816UKEE/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS9816UKEE",
"aliases": [
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR1-Rep1_S219",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR2-Rep1_S225",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR3-Rep1_S261",
"jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR4-Rep1_S267"
],
"audit": {
"ERROR": [
{
"category": "missing measurement set",
"detail": "Auxiliary set [IGVFDS9816UKEE](/auxiliary-sets/IGVFDS9816UKEE/) is not associated with any `measurement_sets`. Auxiliary sets are expected to be associated with a measurement set(s).",
"level": 60,
"level_name": "ERROR",
"name": "audit_missing_measurement_sets",
"path": "/auxiliary-sets/IGVFDS9816UKEE/"
}
],
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM2913DQHN](/in-vitro-systems/IGVFSM2913DQHN/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_sample_missing_publication",
"path": "/in-vitro-systems/IGVFSM2913DQHN/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing files",
"detail": "Auxiliary set [IGVFDS9816UKEE](/auxiliary-sets/IGVFDS9816UKEE/) has no `files`. File sets are expected to have files.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_no_files",
"path": "/auxiliary-sets/IGVFDS9816UKEE/"
}
],
"WARNING": [
{
"category": "missing nucleic acid delivery",
"detail": "In vitro system [IGVFSM2913DQHN](/in-vitro-systems/IGVFSM2913DQHN/) has `construct_library_sets` but is missing `nucleic_acid_delivery`. Samples linked to construct library sets are expected to specify nucleic acid delivery method.",
"level": 40,
"level_name": "WARNING",
"name": "audit_missing_nucleic_acid_delivery",
"path": "/in-vitro-systems/IGVFSM2913DQHN/"
}
]
},
"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"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6351FGNG/",
"accession": "IGVFDS6351FGNG",
"file_set_type": "guide library",
"integrated_content_files": [
{
"@id": "/tabular-files/IGVFFI5924HOIN/",
"accession": "IGVFFI5924HOIN",
"content_type": "guide RNA sequences",
"status": "released",
"summary": "guide RNA sequences"
}
],
"status": "released",
"summary": "guide (sgRNA) library targeting accessible genome regions in many genomic loci"
}
],
"control_for": [],
"creation_timestamp": "2024-05-13T22:38:47.107623+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO0384OZRW/",
"accession": "IGVFDO0384OZRW",
"aliases": [
"igvf:donor_of_HCT116"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "gRNA sequencing",
"files": [],
"input_for": [
"/analysis-sets/IGVFDS1569RNPD/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"measurement_sets": [],
"release_timestamp": "2024-07-10T20:08:04.007903+00:00",
"revoke_detail": "This auxiliary set has been revoked as its files have been moved to the measurement set: /measurement-sets/IGVFDS0528ZIOC/",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2913DQHN/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2913DQHN",
"aliases": [
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR1-Rep1_S219",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR2-Rep1_S225",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR3-Rep1_S261",
"jesse-engreitz:in-vitro-system_CRUDO_CCND1_Auxin0hrs-FF1-BinC-PCR4-Rep1_S267"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"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": "Homo sapiens (male) HCT116 cell line (sorting details: FACS bin C for 35-45% expression of CCND1) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "12",
"status": "revoked",
"submitted_by": {
"@id": "/users/3bd6f74c-8cf3-4c35-a94d-0c7c11654815/",
"title": "Chongyon Park"
},
"summary": "gRNA sequencing",
"uuid": "f3949b3c-2664-470c-ad45-3ee06d534a0c"
}