{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7918VFRY/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7918VFRY",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep1-FACS_Input_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS7918VFRY](/measurement-sets/IGVFDS7918VFRY/) has sequence file(s) [IGVFFI5635XEJV](/sequence-files/IGVFFI5635XEJV/), [IGVFFI3051XCCS](/sequence-files/IGVFFI3051XCCS/), [IGVFFI4536YVST](/sequence-files/IGVFFI4536YVST/), [IGVFFI9382RIZB](/sequence-files/IGVFFI9382RIZB/), [IGVFFI2242MJEB](/sequence-files/IGVFFI2242MJEB/), [IGVFFI6619XWHE](/sequence-files/IGVFFI6619XWHE/), [IGVFFI7600BYCX](/sequence-files/IGVFFI7600BYCX/), [IGVFFI3382BVOT](/sequence-files/IGVFFI3382BVOT/) 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/IGVFDS7918VFRY/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7918VFRY](/measurement-sets/IGVFDS7918VFRY/) has sequence file(s): [IGVFFI5635XEJV](/sequence-files/IGVFFI5635XEJV/), [IGVFFI3051XCCS](/sequence-files/IGVFFI3051XCCS/), [IGVFFI4536YVST](/sequence-files/IGVFFI4536YVST/), [IGVFFI9382RIZB](/sequence-files/IGVFFI9382RIZB/), [IGVFFI2242MJEB](/sequence-files/IGVFFI2242MJEB/), [IGVFFI6619XWHE](/sequence-files/IGVFFI6619XWHE/), [IGVFFI7600BYCX](/sequence-files/IGVFFI7600BYCX/), [IGVFFI3382BVOT](/sequence-files/IGVFFI3382BVOT/) 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/IGVFDS7918VFRY/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7918VFRY](/measurement-sets/IGVFDS7918VFRY/) 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/IGVFDS7918VFRY/"
}
]
},
"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/IGVFDS0861MZYT/",
"accession": "IGVFDS0861MZYT",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-PE2_Exp6_NegControl_AmpliconSequencing"
],
"status": "preview"
}
],
"control_for": [],
"creation_timestamp": "2024-12-01T19:57:59.002369+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI5635XEJV/",
"accession": "IGVFFI5635XEJV",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep1-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T20:40:04.267103+00:00",
"file_format": "fastq",
"file_size": 59233479,
"href": "/sequence-files/IGVFFI5635XEJV/@@download/IGVFFI5635XEJV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/3d0e3864-0843-4fae-b3c7-234fb3bf809f/IGVFFI5635XEJV.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_pool-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep2_S975_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3051XCCS/",
"accession": "IGVFFI3051XCCS",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep1-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T23:04:28.490175+00:00",
"file_format": "fastq",
"file_size": 18555191,
"href": "/sequence-files/IGVFFI3051XCCS/@@download/IGVFFI3051XCCS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/67587adb-40eb-48a5-a851-1ad3c10e73e0/IGVFFI3051XCCS.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_pool-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep2_S975_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4536YVST/",
"accession": "IGVFFI4536YVST",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep1-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T21:21:03.557398+00:00",
"file_format": "fastq",
"file_size": 32654502,
"href": "/sequence-files/IGVFFI4536YVST/@@download/IGVFFI4536YVST.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/81686458-d780-4bfb-943f-6f78cbd5bdf7/IGVFFI4536YVST.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_pool-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep1_S963_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9382RIZB/",
"accession": "IGVFFI9382RIZB",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep1-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T21:24:46.792935+00:00",
"file_format": "fastq",
"file_size": 48858745,
"href": "/sequence-files/IGVFFI9382RIZB/@@download/IGVFFI9382RIZB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/08cd3313-7c69-401d-9a1e-930096e79e7f/IGVFFI9382RIZB.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_pool-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep2_S975_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2242MJEB/",
"accession": "IGVFFI2242MJEB",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep1-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T22:12:20.287635+00:00",
"file_format": "fastq",
"file_size": 13906448,
"href": "/sequence-files/IGVFFI2242MJEB/@@download/IGVFFI2242MJEB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/98d617de-ee2b-41f3-9adc-43d6079b6e07/IGVFFI2242MJEB.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_pool-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep1_S963_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6619XWHE/",
"accession": "IGVFFI6619XWHE",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep1-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T20:36:23.487350+00:00",
"file_format": "fastq",
"file_size": 39125296,
"href": "/sequence-files/IGVFFI6619XWHE/@@download/IGVFFI6619XWHE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/74de6c12-cecd-490a-ad37-b2622d03f711/IGVFFI6619XWHE.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_pool-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep1_S963_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7600BYCX/",
"accession": "IGVFFI7600BYCX",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep1-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T22:15:48.358188+00:00",
"file_format": "fastq",
"file_size": 18688844,
"href": "/sequence-files/IGVFFI7600BYCX/@@download/IGVFFI7600BYCX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/a1312ae9-4096-4e9a-bc07-4a9aa63be3cd/IGVFFI7600BYCX.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_pool-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep2_S975_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3382BVOT/",
"accession": "IGVFFI3382BVOT",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep1-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-01T23:00:55.547465+00:00",
"file_format": "fastq",
"file_size": 12330129,
"href": "/sequence-files/IGVFFI3382BVOT/@@download/IGVFFI3382BVOT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/01/f7c7bc11-da5a-46c1-be63-7e8e44eaa443/IGVFFI3382BVOT.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_pool-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep1_S963_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS7090INDM/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "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"
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9185JHBG/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9185JHBG",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep1-FACS_Input"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS5639ITBS/",
"accession": "IGVFDS5639ITBS",
"file_set_type": "guide library",
"status": "preview",
"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_0001253/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:THP-1"
],
"status": "released",
"summary": "THP-1",
"term_name": "THP-1"
}
],
"status": "preview",
"summary": "THP-1 cell line, male, Homo sapiens modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "preview",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2024-12-01T20:36:23.487350+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": "23826322-daff-49cf-9731-da40ceaeff0a"
}