{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5585MKNA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5585MKNA",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinB_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM9109WXYZ](/in-vitro-systems/IGVFSM9109WXYZ/) has in progress subobject construct library set [IGVFDS6377KNCH](/construct-library-sets/IGVFDS6377KNCH/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM9109WXYZ/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS5585MKNA](/measurement-sets/IGVFDS5585MKNA/) has sequence file(s) [IGVFFI6989LFPW](/sequence-files/IGVFFI6989LFPW/), [IGVFFI9461CCDU](/sequence-files/IGVFFI9461CCDU/), [IGVFFI8132GAUA](/sequence-files/IGVFFI8132GAUA/), [IGVFFI2567YPPK](/sequence-files/IGVFFI2567YPPK/), [IGVFFI9702WSMS](/sequence-files/IGVFFI9702WSMS/), [IGVFFI2572NCLL](/sequence-files/IGVFFI2572NCLL/), [IGVFFI9559EYAY](/sequence-files/IGVFFI9559EYAY/), [IGVFFI3322NVDG](/sequence-files/IGVFFI3322NVDG/) 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": "/measurement-sets/IGVFDS5585MKNA/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5585MKNA](/measurement-sets/IGVFDS5585MKNA/) has sequence file(s): [IGVFFI6989LFPW](/sequence-files/IGVFFI6989LFPW/), [IGVFFI9461CCDU](/sequence-files/IGVFFI9461CCDU/), [IGVFFI8132GAUA](/sequence-files/IGVFFI8132GAUA/), [IGVFFI2567YPPK](/sequence-files/IGVFFI2567YPPK/), [IGVFFI9702WSMS](/sequence-files/IGVFFI9702WSMS/), [IGVFFI2572NCLL](/sequence-files/IGVFFI2572NCLL/), [IGVFFI9559EYAY](/sequence-files/IGVFFI9559EYAY/), [IGVFFI3322NVDG](/sequence-files/IGVFFI3322NVDG/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS5585MKNA/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5585MKNA](/measurement-sets/IGVFDS5585MKNA/) 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": 40,
"level_name": "WARNING",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS5585MKNA/"
}
]
},
"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/IGVFDS9477ARWI/",
"accession": "IGVFDS9477ARWI",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-Jurkat-PE2_Exp1_NegControl_AmpliconSequencing",
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-Jurkat-PE2_Exp1_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"creation_timestamp": "2023-12-01T00:02:53.236361+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1080XFGV/",
"accession": "IGVFDO1080XFGV",
"aliases": [
"igvf:donor_of_Jurkat"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI6989LFPW/",
"accession": "IGVFFI6989LFPW",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinB-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:24:37.936083+00:00",
"file_format": "fastq",
"file_size": 3248383,
"href": "/sequence-files/IGVFFI6989LFPW/@@download/IGVFFI6989LFPW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/5d9db514-3320-4af5-8c68-80429794fc4a/IGVFFI6989LFPW.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S2-BioRep1-FFRep1-BinB-PCRrep2_S58_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9461CCDU/",
"accession": "IGVFFI9461CCDU",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinB-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:59:12.100049+00:00",
"file_format": "fastq",
"file_size": 14647193,
"href": "/sequence-files/IGVFFI9461CCDU/@@download/IGVFFI9461CCDU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a248e95a-84fa-4728-9e4e-4766331dee12/IGVFFI9461CCDU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S2-BioRep1-FFRep1-BinB-PCRrep2_S58_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8132GAUA/",
"accession": "IGVFFI8132GAUA",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinB-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:12:02.361860+00:00",
"file_format": "fastq",
"file_size": 3383966,
"href": "/sequence-files/IGVFFI8132GAUA/@@download/IGVFFI8132GAUA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/483a3da0-732d-4170-bf6d-9c94ddd9c4a1/IGVFFI8132GAUA.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S2-BioRep1-FFRep1-BinB-PCRrep2_S58_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2567YPPK/",
"accession": "IGVFFI2567YPPK",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinB-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:05:48.940210+00:00",
"file_format": "fastq",
"file_size": 3356699,
"href": "/sequence-files/IGVFFI2567YPPK/@@download/IGVFFI2567YPPK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/01f49859-72e6-4d99-93d7-33596f0e0619/IGVFFI2567YPPK.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S2-BioRep1-FFRep1-BinB-PCRrep1_S2_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9702WSMS/",
"accession": "IGVFFI9702WSMS",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinB-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:18:17.287416+00:00",
"file_format": "fastq",
"file_size": 3254888,
"href": "/sequence-files/IGVFFI9702WSMS/@@download/IGVFFI9702WSMS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/57b2e373-85f7-40ce-8196-a5819b36d370/IGVFFI9702WSMS.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S2-BioRep1-FFRep1-BinB-PCRrep1_S2_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2572NCLL/",
"accession": "IGVFFI2572NCLL",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinB-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:40:00.182579+00:00",
"file_format": "fastq",
"file_size": 7979763,
"href": "/sequence-files/IGVFFI2572NCLL/@@download/IGVFFI2572NCLL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e20f45c9-6c50-419d-b782-3a0c61ed0da4/IGVFFI2572NCLL.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S2-BioRep1-FFRep1-BinB-PCRrep1_S2_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9559EYAY/",
"accession": "IGVFFI9559EYAY",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinB-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:46:20.403084+00:00",
"file_format": "fastq",
"file_size": 8068050,
"href": "/sequence-files/IGVFFI9559EYAY/@@download/IGVFFI9559EYAY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/ec577f7a-97f0-41bc-ac2e-1c7c007bc052/IGVFFI9559EYAY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S2-BioRep1-FFRep1-BinB-PCRrep2_S58_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3322NVDG/",
"accession": "IGVFFI3322NVDG",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinB-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:52:39.500240+00:00",
"file_format": "fastq",
"file_size": 14658847,
"href": "/sequence-files/IGVFFI3322NVDG/@@download/IGVFFI3322NVDG.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2dbf6b16-9588-4a78-af61-f449fcf10346/IGVFFI3322NVDG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S2-BioRep1-FFRep1-BinB-PCRrep1_S2_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS9162RHFP/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set. This measurement set previously used Variant FlowFISH as a preferred_assay_title, but this enum is now removed. So it has been defaulted to Variant-EFFECTS.",
"preferred_assay_title": "Variant-EFFECTS",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"release_timestamp": "2023-12-20T23:04:02.993170+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9109WXYZ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9109WXYZ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinB"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6377KNCH/",
"accession": "IGVFDS6377KNCH",
"file_set_type": "guide library",
"status": "in progress",
"summary": "guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0002796/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:Jurkat"
],
"status": "released",
"summary": "Jurkat",
"term_name": "Jurkat"
}
],
"status": "released",
"summary": "Jurkat cell line, male, Homo sapiens (sorting details: FACS bin for 11-20% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T18:40:00.182579+00:00",
"summary": "CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"targeted_genes": [
{
"@id": "/genes/ENSG00000108179/",
"geneid": "ENSG00000108179",
"name": "peptidylprolyl isomerase F",
"status": "released",
"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": "826a218c-8b12-4d0a-9b24-083f4ea202c9"
}