{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8517SHZG/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8517SHZG",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinC_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM8427KPPU](/in-vitro-systems/IGVFSM8427KPPU/) has in progress subobject construct library set [IGVFDS6982DESN](/construct-library-sets/IGVFDS6982DESN/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM8427KPPU/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS8517SHZG](/measurement-sets/IGVFDS8517SHZG/) has in progress subobject auxiliary set [IGVFDS5308OHVA](/auxiliary-sets/IGVFDS5308OHVA/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS8517SHZG/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS5308OHVA](/auxiliary-sets/IGVFDS5308OHVA/) has sequence file(s): [IGVFFI6557BGFE](/sequence-files/IGVFFI6557BGFE/), [IGVFFI5299LSFY](/sequence-files/IGVFFI5299LSFY/), [IGVFFI4306LMZR](/sequence-files/IGVFFI4306LMZR/), [IGVFFI0533BEBH](/sequence-files/IGVFFI0533BEBH/), [IGVFFI8463GSUS](/sequence-files/IGVFFI8463GSUS/), [IGVFFI0755NBOR](/sequence-files/IGVFFI0755NBOR/), [IGVFFI2537RBCD](/sequence-files/IGVFFI2537RBCD/), [IGVFFI1236IUVB](/sequence-files/IGVFFI1236IUVB/), [IGVFFI0786YLTV](/sequence-files/IGVFFI0786YLTV/), [IGVFFI8130BHAE](/sequence-files/IGVFFI8130BHAE/), [IGVFFI8401IBDT](/sequence-files/IGVFFI8401IBDT/), [IGVFFI6819OZVW](/sequence-files/IGVFFI6819OZVW/), [IGVFFI9531ETAI](/sequence-files/IGVFFI9531ETAI/), [IGVFFI0800EEXN](/sequence-files/IGVFFI0800EEXN/), [IGVFFI5190IWYZ](/sequence-files/IGVFFI5190IWYZ/), [IGVFFI2591WMRY](/sequence-files/IGVFFI2591WMRY/), [IGVFFI3064OWJY](/sequence-files/IGVFFI3064OWJY/), [IGVFFI0767UQNW](/sequence-files/IGVFFI0767UQNW/), [IGVFFI1617WSPF](/sequence-files/IGVFFI1617WSPF/), [IGVFFI6884FQGD](/sequence-files/IGVFFI6884FQGD/), [IGVFFI4368IFSI](/sequence-files/IGVFFI4368IFSI/), [IGVFFI9869AHBS](/sequence-files/IGVFFI9869AHBS/), [IGVFFI4399POXT](/sequence-files/IGVFFI4399POXT/), [IGVFFI5652NRME](/sequence-files/IGVFFI5652NRME/), [IGVFFI9788TNVD](/sequence-files/IGVFFI9788TNVD/), [IGVFFI0605OUSO](/sequence-files/IGVFFI0605OUSO/), [IGVFFI4930WDWS](/sequence-files/IGVFFI4930WDWS/), [IGVFFI4522GLML](/sequence-files/IGVFFI4522GLML/), [IGVFFI2117VXUO](/sequence-files/IGVFFI2117VXUO/), [IGVFFI9825WHZM](/sequence-files/IGVFFI9825WHZM/), [IGVFFI5184USTP](/sequence-files/IGVFFI5184USTP/), [IGVFFI8614ATCQ](/sequence-files/IGVFFI8614ATCQ/), [IGVFFI6952BIQE](/sequence-files/IGVFFI6952BIQE/), [IGVFFI4892OWDC](/sequence-files/IGVFFI4892OWDC/), [IGVFFI4077AOQG](/sequence-files/IGVFFI4077AOQG/), [IGVFFI1411ARZI](/sequence-files/IGVFFI1411ARZI/), [IGVFFI2266UYYN](/sequence-files/IGVFFI2266UYYN/), [IGVFFI9845WTKK](/sequence-files/IGVFFI9845WTKK/), [IGVFFI8538IGQA](/sequence-files/IGVFFI8538IGQA/), [IGVFFI6031NWVD](/sequence-files/IGVFFI6031NWVD/), [IGVFFI6994LGFG](/sequence-files/IGVFFI6994LGFG/), [IGVFFI8132FNYQ](/sequence-files/IGVFFI8132FNYQ/), [IGVFFI1457IZNE](/sequence-files/IGVFFI1457IZNE/), [IGVFFI4290TUGE](/sequence-files/IGVFFI4290TUGE/), [IGVFFI1655EAEO](/sequence-files/IGVFFI1655EAEO/), [IGVFFI5024QCKP](/sequence-files/IGVFFI5024QCKP/), [IGVFFI5799YYQG](/sequence-files/IGVFFI5799YYQG/), [IGVFFI8614OVLD](/sequence-files/IGVFFI8614OVLD/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS5308OHVA/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS8517SHZG](/measurement-sets/IGVFDS8517SHZG/) has no cell sorting `auxiliary_sets`. CRISPR-based measurement sets that utilize flow cytometry are expected to link to a cell sorting auxiliary set.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS8517SHZG/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS5308OHVA](/auxiliary-sets/IGVFDS5308OHVA/) has sequence file(s) [IGVFFI6557BGFE](/sequence-files/IGVFFI6557BGFE/), [IGVFFI5299LSFY](/sequence-files/IGVFFI5299LSFY/), [IGVFFI4306LMZR](/sequence-files/IGVFFI4306LMZR/), [IGVFFI0533BEBH](/sequence-files/IGVFFI0533BEBH/), [IGVFFI8463GSUS](/sequence-files/IGVFFI8463GSUS/), [IGVFFI0755NBOR](/sequence-files/IGVFFI0755NBOR/), [IGVFFI2537RBCD](/sequence-files/IGVFFI2537RBCD/), [IGVFFI1236IUVB](/sequence-files/IGVFFI1236IUVB/), [IGVFFI0786YLTV](/sequence-files/IGVFFI0786YLTV/), [IGVFFI8130BHAE](/sequence-files/IGVFFI8130BHAE/), [IGVFFI8401IBDT](/sequence-files/IGVFFI8401IBDT/), [IGVFFI6819OZVW](/sequence-files/IGVFFI6819OZVW/), [IGVFFI9531ETAI](/sequence-files/IGVFFI9531ETAI/), [IGVFFI0800EEXN](/sequence-files/IGVFFI0800EEXN/), [IGVFFI5190IWYZ](/sequence-files/IGVFFI5190IWYZ/), [IGVFFI2591WMRY](/sequence-files/IGVFFI2591WMRY/), [IGVFFI3064OWJY](/sequence-files/IGVFFI3064OWJY/), [IGVFFI0767UQNW](/sequence-files/IGVFFI0767UQNW/), [IGVFFI1617WSPF](/sequence-files/IGVFFI1617WSPF/), [IGVFFI6884FQGD](/sequence-files/IGVFFI6884FQGD/), [IGVFFI4368IFSI](/sequence-files/IGVFFI4368IFSI/), [IGVFFI9869AHBS](/sequence-files/IGVFFI9869AHBS/), [IGVFFI4399POXT](/sequence-files/IGVFFI4399POXT/), [IGVFFI5652NRME](/sequence-files/IGVFFI5652NRME/), [IGVFFI9788TNVD](/sequence-files/IGVFFI9788TNVD/), [IGVFFI0605OUSO](/sequence-files/IGVFFI0605OUSO/), [IGVFFI4930WDWS](/sequence-files/IGVFFI4930WDWS/), [IGVFFI4522GLML](/sequence-files/IGVFFI4522GLML/), [IGVFFI2117VXUO](/sequence-files/IGVFFI2117VXUO/), [IGVFFI9825WHZM](/sequence-files/IGVFFI9825WHZM/), [IGVFFI5184USTP](/sequence-files/IGVFFI5184USTP/), [IGVFFI8614ATCQ](/sequence-files/IGVFFI8614ATCQ/), [IGVFFI6952BIQE](/sequence-files/IGVFFI6952BIQE/), [IGVFFI4892OWDC](/sequence-files/IGVFFI4892OWDC/), [IGVFFI4077AOQG](/sequence-files/IGVFFI4077AOQG/), [IGVFFI1411ARZI](/sequence-files/IGVFFI1411ARZI/), [IGVFFI2266UYYN](/sequence-files/IGVFFI2266UYYN/), [IGVFFI9845WTKK](/sequence-files/IGVFFI9845WTKK/), [IGVFFI8538IGQA](/sequence-files/IGVFFI8538IGQA/), [IGVFFI6031NWVD](/sequence-files/IGVFFI6031NWVD/), [IGVFFI6994LGFG](/sequence-files/IGVFFI6994LGFG/), [IGVFFI8132FNYQ](/sequence-files/IGVFFI8132FNYQ/), [IGVFFI1457IZNE](/sequence-files/IGVFFI1457IZNE/), [IGVFFI4290TUGE](/sequence-files/IGVFFI4290TUGE/), [IGVFFI1655EAEO](/sequence-files/IGVFFI1655EAEO/), [IGVFFI5024QCKP](/sequence-files/IGVFFI5024QCKP/), [IGVFFI5799YYQG](/sequence-files/IGVFFI5799YYQG/), [IGVFFI8614OVLD](/sequence-files/IGVFFI8614OVLD/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 40,
"level_name": "WARNING",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS5308OHVA/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS5308OHVA](/auxiliary-sets/IGVFDS5308OHVA/) 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": 40,
"level_name": "WARNING",
"name": "audit_input_file_set_for",
"path": "/auxiliary-sets/IGVFDS5308OHVA/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS5308OHVA/",
"accession": "IGVFDS5308OHVA",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinC_AmpliconSequencing_AuxiliarySet"
],
"file_set_type": "variant sequencing"
}
],
"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_file_sets": [
{
"@id": "/measurement-sets/IGVFDS5864UGFT/",
"accession": "IGVFDS5864UGFT",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:50:00.675615+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "experimental data",
"files": [],
"input_file_set_for": [
"/analysis-sets/IGVFDS3423PSID/"
],
"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": "Variant FlowFISH",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"release_timestamp": "2023-12-20T23:06:41.494040+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8427KPPU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8427KPPU",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep2-BinC"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6982DESN/",
"accession": "IGVFDS6982DESN",
"file_set_type": "guide library",
"summary": "Guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:THP-1"
],
"status": "released",
"summary": "THP-1",
"term_name": "THP-1"
}
],
"status": "released",
"summary": "THP-1 cell line, male, Homo sapiens (sorting details: FACS bin for 51-75% expression of PPIF) modified with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "21",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T22:15:47.903908+00:00",
"summary": "Variant FlowFISH integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"targeted_genes": [
{
"@id": "/genes/ENSG00000108179/",
"geneid": "ENSG00000108179",
"name": "peptidylprolyl isomerase F",
"symbol": "PPIF",
"synonyms": [
"rotamase F",
"CYP3",
"cyclophilin F",
"mitochondrial cyclophilin",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"CypD",
"Cyp-D",
"cyclophilin 3",
"cyclophilin D",
"CyP-M",
"peptidyl-prolyl cis-trans isomerase F, mitochondrial",
"PPIase F"
]
}
],
"uuid": "c72d068b-98e8-4a24-adaf-7c5879e3c53b"
}