{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8356GTHO/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8356GTHO",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinD_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 [IGVFDS8356GTHO](/measurement-sets/IGVFDS8356GTHO/) has in progress subobject auxiliary set [IGVFDS7397DNHS](/auxiliary-sets/IGVFDS7397DNHS/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS8356GTHO/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM9715TWHE](/in-vitro-systems/IGVFSM9715TWHE/) 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/IGVFSM9715TWHE/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS8356GTHO](/measurement-sets/IGVFDS8356GTHO/) 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/IGVFDS8356GTHO/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS7397DNHS](/auxiliary-sets/IGVFDS7397DNHS/) has sequence file(s): [IGVFFI6931LKTV](/sequence-files/IGVFFI6931LKTV/), [IGVFFI4568GFTG](/sequence-files/IGVFFI4568GFTG/), [IGVFFI9579PKRX](/sequence-files/IGVFFI9579PKRX/), [IGVFFI2703GDGR](/sequence-files/IGVFFI2703GDGR/), [IGVFFI5166OCPX](/sequence-files/IGVFFI5166OCPX/), [IGVFFI8982QDFT](/sequence-files/IGVFFI8982QDFT/), [IGVFFI0467ULNZ](/sequence-files/IGVFFI0467ULNZ/), [IGVFFI3311SHVZ](/sequence-files/IGVFFI3311SHVZ/), [IGVFFI0925HJEU](/sequence-files/IGVFFI0925HJEU/), [IGVFFI8742CHFV](/sequence-files/IGVFFI8742CHFV/), [IGVFFI8982WTIO](/sequence-files/IGVFFI8982WTIO/), [IGVFFI2513VZJW](/sequence-files/IGVFFI2513VZJW/), [IGVFFI0934INHF](/sequence-files/IGVFFI0934INHF/), [IGVFFI8177MYCI](/sequence-files/IGVFFI8177MYCI/), [IGVFFI6873EQWD](/sequence-files/IGVFFI6873EQWD/), [IGVFFI9697JRCR](/sequence-files/IGVFFI9697JRCR/), [IGVFFI9244ZVIG](/sequence-files/IGVFFI9244ZVIG/), [IGVFFI3157OMHJ](/sequence-files/IGVFFI3157OMHJ/), [IGVFFI4593AFPG](/sequence-files/IGVFFI4593AFPG/), [IGVFFI9114ALHR](/sequence-files/IGVFFI9114ALHR/), [IGVFFI0046QKFS](/sequence-files/IGVFFI0046QKFS/), [IGVFFI4012DQEV](/sequence-files/IGVFFI4012DQEV/), [IGVFFI1148TMWC](/sequence-files/IGVFFI1148TMWC/), [IGVFFI8979BVWT](/sequence-files/IGVFFI8979BVWT/), [IGVFFI5022BOGU](/sequence-files/IGVFFI5022BOGU/), [IGVFFI7401KWUE](/sequence-files/IGVFFI7401KWUE/), [IGVFFI2452QHHG](/sequence-files/IGVFFI2452QHHG/), [IGVFFI1452CSHN](/sequence-files/IGVFFI1452CSHN/), [IGVFFI7897FQDS](/sequence-files/IGVFFI7897FQDS/), [IGVFFI9961WQGA](/sequence-files/IGVFFI9961WQGA/), [IGVFFI6602PDFK](/sequence-files/IGVFFI6602PDFK/), [IGVFFI0959UBMT](/sequence-files/IGVFFI0959UBMT/), [IGVFFI1899RVQH](/sequence-files/IGVFFI1899RVQH/), [IGVFFI7743SDGS](/sequence-files/IGVFFI7743SDGS/), [IGVFFI4785YHXU](/sequence-files/IGVFFI4785YHXU/), [IGVFFI2057GMQO](/sequence-files/IGVFFI2057GMQO/), [IGVFFI8163LYDI](/sequence-files/IGVFFI8163LYDI/), [IGVFFI6530CELH](/sequence-files/IGVFFI6530CELH/), [IGVFFI9164YJYG](/sequence-files/IGVFFI9164YJYG/), [IGVFFI6523BPLR](/sequence-files/IGVFFI6523BPLR/), [IGVFFI0669UVXO](/sequence-files/IGVFFI0669UVXO/), [IGVFFI6115UFLP](/sequence-files/IGVFFI6115UFLP/), [IGVFFI4610VZCI](/sequence-files/IGVFFI4610VZCI/), [IGVFFI0142NJLL](/sequence-files/IGVFFI0142NJLL/), [IGVFFI0195KDJP](/sequence-files/IGVFFI0195KDJP/), [IGVFFI0265AZWF](/sequence-files/IGVFFI0265AZWF/), [IGVFFI8534SVUL](/sequence-files/IGVFFI8534SVUL/), [IGVFFI1565JNTM](/sequence-files/IGVFFI1565JNTM/) 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/IGVFDS7397DNHS/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS7397DNHS](/auxiliary-sets/IGVFDS7397DNHS/) has sequence file(s) [IGVFFI6931LKTV](/sequence-files/IGVFFI6931LKTV/), [IGVFFI4568GFTG](/sequence-files/IGVFFI4568GFTG/), [IGVFFI9579PKRX](/sequence-files/IGVFFI9579PKRX/), [IGVFFI2703GDGR](/sequence-files/IGVFFI2703GDGR/), [IGVFFI5166OCPX](/sequence-files/IGVFFI5166OCPX/), [IGVFFI8982QDFT](/sequence-files/IGVFFI8982QDFT/), [IGVFFI0467ULNZ](/sequence-files/IGVFFI0467ULNZ/), [IGVFFI3311SHVZ](/sequence-files/IGVFFI3311SHVZ/), [IGVFFI0925HJEU](/sequence-files/IGVFFI0925HJEU/), [IGVFFI8742CHFV](/sequence-files/IGVFFI8742CHFV/), [IGVFFI8982WTIO](/sequence-files/IGVFFI8982WTIO/), [IGVFFI2513VZJW](/sequence-files/IGVFFI2513VZJW/), [IGVFFI0934INHF](/sequence-files/IGVFFI0934INHF/), [IGVFFI8177MYCI](/sequence-files/IGVFFI8177MYCI/), [IGVFFI6873EQWD](/sequence-files/IGVFFI6873EQWD/), [IGVFFI9697JRCR](/sequence-files/IGVFFI9697JRCR/), [IGVFFI9244ZVIG](/sequence-files/IGVFFI9244ZVIG/), [IGVFFI3157OMHJ](/sequence-files/IGVFFI3157OMHJ/), [IGVFFI4593AFPG](/sequence-files/IGVFFI4593AFPG/), [IGVFFI9114ALHR](/sequence-files/IGVFFI9114ALHR/), [IGVFFI0046QKFS](/sequence-files/IGVFFI0046QKFS/), [IGVFFI4012DQEV](/sequence-files/IGVFFI4012DQEV/), [IGVFFI1148TMWC](/sequence-files/IGVFFI1148TMWC/), [IGVFFI8979BVWT](/sequence-files/IGVFFI8979BVWT/), [IGVFFI5022BOGU](/sequence-files/IGVFFI5022BOGU/), [IGVFFI7401KWUE](/sequence-files/IGVFFI7401KWUE/), [IGVFFI2452QHHG](/sequence-files/IGVFFI2452QHHG/), [IGVFFI1452CSHN](/sequence-files/IGVFFI1452CSHN/), [IGVFFI7897FQDS](/sequence-files/IGVFFI7897FQDS/), [IGVFFI9961WQGA](/sequence-files/IGVFFI9961WQGA/), [IGVFFI6602PDFK](/sequence-files/IGVFFI6602PDFK/), [IGVFFI0959UBMT](/sequence-files/IGVFFI0959UBMT/), [IGVFFI1899RVQH](/sequence-files/IGVFFI1899RVQH/), [IGVFFI7743SDGS](/sequence-files/IGVFFI7743SDGS/), [IGVFFI4785YHXU](/sequence-files/IGVFFI4785YHXU/), [IGVFFI2057GMQO](/sequence-files/IGVFFI2057GMQO/), [IGVFFI8163LYDI](/sequence-files/IGVFFI8163LYDI/), [IGVFFI6530CELH](/sequence-files/IGVFFI6530CELH/), [IGVFFI9164YJYG](/sequence-files/IGVFFI9164YJYG/), [IGVFFI6523BPLR](/sequence-files/IGVFFI6523BPLR/), [IGVFFI0669UVXO](/sequence-files/IGVFFI0669UVXO/), [IGVFFI6115UFLP](/sequence-files/IGVFFI6115UFLP/), [IGVFFI4610VZCI](/sequence-files/IGVFFI4610VZCI/), [IGVFFI0142NJLL](/sequence-files/IGVFFI0142NJLL/), [IGVFFI0195KDJP](/sequence-files/IGVFFI0195KDJP/), [IGVFFI0265AZWF](/sequence-files/IGVFFI0265AZWF/), [IGVFFI8534SVUL](/sequence-files/IGVFFI8534SVUL/), [IGVFFI1565JNTM](/sequence-files/IGVFFI1565JNTM/) 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/IGVFDS7397DNHS/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS7397DNHS](/auxiliary-sets/IGVFDS7397DNHS/) 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/IGVFDS7397DNHS/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS7397DNHS/",
"accession": "IGVFDS7397DNHS",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinD_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": "2023-12-01T00:05:36.165833+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": "2023-12-20T23:06:38.520594+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9715TWHE/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9715TWHE",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinD"
],
"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 76-100% expression of PPIF) modified with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "20",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T19:51:13.468743+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": "f2163f4b-b67b-45d3-ab31-c5171b60b5ab"
}