{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6551IWAB/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6551IWAB",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-BinA_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 measurement set [IGVFDS6551IWAB](/measurement-sets/IGVFDS6551IWAB/) has in progress subobject auxiliary set [IGVFDS8783FMQT](/auxiliary-sets/IGVFDS8783FMQT/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS6551IWAB/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM5332OJBP](/in-vitro-systems/IGVFSM5332OJBP/) 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/IGVFSM5332OJBP/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8783FMQT](/auxiliary-sets/IGVFDS8783FMQT/) has sequence file(s): [IGVFFI3288MFCS](/sequence-files/IGVFFI3288MFCS/), [IGVFFI8233PPUK](/sequence-files/IGVFFI8233PPUK/), [IGVFFI6854MJAP](/sequence-files/IGVFFI6854MJAP/), [IGVFFI7933IYVE](/sequence-files/IGVFFI7933IYVE/), [IGVFFI5132BDBC](/sequence-files/IGVFFI5132BDBC/), [IGVFFI5656GEPY](/sequence-files/IGVFFI5656GEPY/), [IGVFFI1561JFQT](/sequence-files/IGVFFI1561JFQT/), [IGVFFI4562JQNV](/sequence-files/IGVFFI4562JQNV/), [IGVFFI4701JQEW](/sequence-files/IGVFFI4701JQEW/), [IGVFFI6834VZSM](/sequence-files/IGVFFI6834VZSM/), [IGVFFI6195OWGE](/sequence-files/IGVFFI6195OWGE/), [IGVFFI5292YDSA](/sequence-files/IGVFFI5292YDSA/), [IGVFFI0571EHWP](/sequence-files/IGVFFI0571EHWP/), [IGVFFI1902DWAV](/sequence-files/IGVFFI1902DWAV/), [IGVFFI4220NRHS](/sequence-files/IGVFFI4220NRHS/), [IGVFFI8927UFJE](/sequence-files/IGVFFI8927UFJE/), [IGVFFI1988JJZW](/sequence-files/IGVFFI1988JJZW/), [IGVFFI1851AWVK](/sequence-files/IGVFFI1851AWVK/), [IGVFFI5527MKJZ](/sequence-files/IGVFFI5527MKJZ/), [IGVFFI9560RXBN](/sequence-files/IGVFFI9560RXBN/), [IGVFFI9563QOIW](/sequence-files/IGVFFI9563QOIW/), [IGVFFI9161HEEW](/sequence-files/IGVFFI9161HEEW/), [IGVFFI5328JUZM](/sequence-files/IGVFFI5328JUZM/), [IGVFFI3505PHKN](/sequence-files/IGVFFI3505PHKN/), [IGVFFI0037IZST](/sequence-files/IGVFFI0037IZST/), [IGVFFI9739KMAC](/sequence-files/IGVFFI9739KMAC/), [IGVFFI0800KGCO](/sequence-files/IGVFFI0800KGCO/), [IGVFFI6671PASM](/sequence-files/IGVFFI6671PASM/), [IGVFFI7681UWKW](/sequence-files/IGVFFI7681UWKW/), [IGVFFI9542CZEE](/sequence-files/IGVFFI9542CZEE/), [IGVFFI9009WQGJ](/sequence-files/IGVFFI9009WQGJ/), [IGVFFI0486RTYP](/sequence-files/IGVFFI0486RTYP/), [IGVFFI4203HDZI](/sequence-files/IGVFFI4203HDZI/), [IGVFFI1140VDZK](/sequence-files/IGVFFI1140VDZK/), [IGVFFI9969KUJW](/sequence-files/IGVFFI9969KUJW/), [IGVFFI9298EPYB](/sequence-files/IGVFFI9298EPYB/), [IGVFFI5989RIMB](/sequence-files/IGVFFI5989RIMB/), [IGVFFI6671TGNU](/sequence-files/IGVFFI6671TGNU/), [IGVFFI0907WDMW](/sequence-files/IGVFFI0907WDMW/), [IGVFFI5190VCAH](/sequence-files/IGVFFI5190VCAH/), [IGVFFI2308CLIM](/sequence-files/IGVFFI2308CLIM/), [IGVFFI6036DQAR](/sequence-files/IGVFFI6036DQAR/), [IGVFFI3331AGQL](/sequence-files/IGVFFI3331AGQL/), [IGVFFI2974SNGN](/sequence-files/IGVFFI2974SNGN/), [IGVFFI8672EIFC](/sequence-files/IGVFFI8672EIFC/), [IGVFFI5986KERP](/sequence-files/IGVFFI5986KERP/), [IGVFFI6691IDNN](/sequence-files/IGVFFI6691IDNN/), [IGVFFI1060GPOW](/sequence-files/IGVFFI1060GPOW/) 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/IGVFDS8783FMQT/"
},
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6551IWAB](/measurement-sets/IGVFDS6551IWAB/) 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/IGVFDS6551IWAB/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8783FMQT](/auxiliary-sets/IGVFDS8783FMQT/) has sequence file(s) [IGVFFI3288MFCS](/sequence-files/IGVFFI3288MFCS/), [IGVFFI8233PPUK](/sequence-files/IGVFFI8233PPUK/), [IGVFFI6854MJAP](/sequence-files/IGVFFI6854MJAP/), [IGVFFI7933IYVE](/sequence-files/IGVFFI7933IYVE/), [IGVFFI5132BDBC](/sequence-files/IGVFFI5132BDBC/), [IGVFFI5656GEPY](/sequence-files/IGVFFI5656GEPY/), [IGVFFI1561JFQT](/sequence-files/IGVFFI1561JFQT/), [IGVFFI4562JQNV](/sequence-files/IGVFFI4562JQNV/), [IGVFFI4701JQEW](/sequence-files/IGVFFI4701JQEW/), [IGVFFI6834VZSM](/sequence-files/IGVFFI6834VZSM/), [IGVFFI6195OWGE](/sequence-files/IGVFFI6195OWGE/), [IGVFFI5292YDSA](/sequence-files/IGVFFI5292YDSA/), [IGVFFI0571EHWP](/sequence-files/IGVFFI0571EHWP/), [IGVFFI1902DWAV](/sequence-files/IGVFFI1902DWAV/), [IGVFFI4220NRHS](/sequence-files/IGVFFI4220NRHS/), [IGVFFI8927UFJE](/sequence-files/IGVFFI8927UFJE/), [IGVFFI1988JJZW](/sequence-files/IGVFFI1988JJZW/), [IGVFFI1851AWVK](/sequence-files/IGVFFI1851AWVK/), [IGVFFI5527MKJZ](/sequence-files/IGVFFI5527MKJZ/), [IGVFFI9560RXBN](/sequence-files/IGVFFI9560RXBN/), [IGVFFI9563QOIW](/sequence-files/IGVFFI9563QOIW/), [IGVFFI9161HEEW](/sequence-files/IGVFFI9161HEEW/), [IGVFFI5328JUZM](/sequence-files/IGVFFI5328JUZM/), [IGVFFI3505PHKN](/sequence-files/IGVFFI3505PHKN/), [IGVFFI0037IZST](/sequence-files/IGVFFI0037IZST/), [IGVFFI9739KMAC](/sequence-files/IGVFFI9739KMAC/), [IGVFFI0800KGCO](/sequence-files/IGVFFI0800KGCO/), [IGVFFI6671PASM](/sequence-files/IGVFFI6671PASM/), [IGVFFI7681UWKW](/sequence-files/IGVFFI7681UWKW/), [IGVFFI9542CZEE](/sequence-files/IGVFFI9542CZEE/), [IGVFFI9009WQGJ](/sequence-files/IGVFFI9009WQGJ/), [IGVFFI0486RTYP](/sequence-files/IGVFFI0486RTYP/), [IGVFFI4203HDZI](/sequence-files/IGVFFI4203HDZI/), [IGVFFI1140VDZK](/sequence-files/IGVFFI1140VDZK/), [IGVFFI9969KUJW](/sequence-files/IGVFFI9969KUJW/), [IGVFFI9298EPYB](/sequence-files/IGVFFI9298EPYB/), [IGVFFI5989RIMB](/sequence-files/IGVFFI5989RIMB/), [IGVFFI6671TGNU](/sequence-files/IGVFFI6671TGNU/), [IGVFFI0907WDMW](/sequence-files/IGVFFI0907WDMW/), [IGVFFI5190VCAH](/sequence-files/IGVFFI5190VCAH/), [IGVFFI2308CLIM](/sequence-files/IGVFFI2308CLIM/), [IGVFFI6036DQAR](/sequence-files/IGVFFI6036DQAR/), [IGVFFI3331AGQL](/sequence-files/IGVFFI3331AGQL/), [IGVFFI2974SNGN](/sequence-files/IGVFFI2974SNGN/), [IGVFFI8672EIFC](/sequence-files/IGVFFI8672EIFC/), [IGVFFI5986KERP](/sequence-files/IGVFFI5986KERP/), [IGVFFI6691IDNN](/sequence-files/IGVFFI6691IDNN/), [IGVFFI1060GPOW](/sequence-files/IGVFFI1060GPOW/) 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/IGVFDS8783FMQT/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS8783FMQT](/auxiliary-sets/IGVFDS8783FMQT/) 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/IGVFDS8783FMQT/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8783FMQT/",
"accession": "IGVFDS8783FMQT",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-BinA_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": "2023-11-30T22:49:41.465382+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": "2023-12-20T23:06:54.409511+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5332OJBP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5332OJBP",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep3-BinA"
],
"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 0-25% 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": "2023-12-05T20:29:35.132817+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": "7f268ade-8659-48f4-9923-24c5bffaa753"
}