{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1171XPUF/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1171XPUF",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-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 [IGVFDS1171XPUF](/measurement-sets/IGVFDS1171XPUF/) has sequence file(s) [IGVFFI2267FEGT](/sequence-files/IGVFFI2267FEGT/), [IGVFFI6689GUPV](/sequence-files/IGVFFI6689GUPV/), [IGVFFI8463SZQL](/sequence-files/IGVFFI8463SZQL/), [IGVFFI6227NOXW](/sequence-files/IGVFFI6227NOXW/), [IGVFFI4905QDDN](/sequence-files/IGVFFI4905QDDN/), [IGVFFI9012STWQ](/sequence-files/IGVFFI9012STWQ/), [IGVFFI6077XTTA](/sequence-files/IGVFFI6077XTTA/), [IGVFFI9485OHPE](/sequence-files/IGVFFI9485OHPE/) 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/IGVFDS1171XPUF/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1171XPUF](/measurement-sets/IGVFDS1171XPUF/) has sequence file(s): [IGVFFI2267FEGT](/sequence-files/IGVFFI2267FEGT/), [IGVFFI6689GUPV](/sequence-files/IGVFFI6689GUPV/), [IGVFFI8463SZQL](/sequence-files/IGVFFI8463SZQL/), [IGVFFI6227NOXW](/sequence-files/IGVFFI6227NOXW/), [IGVFFI4905QDDN](/sequence-files/IGVFFI4905QDDN/), [IGVFFI9012STWQ](/sequence-files/IGVFFI9012STWQ/), [IGVFFI6077XTTA](/sequence-files/IGVFFI6077XTTA/), [IGVFFI9485OHPE](/sequence-files/IGVFFI9485OHPE/) 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/IGVFDS1171XPUF/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1171XPUF](/measurement-sets/IGVFDS1171XPUF/) 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/IGVFDS1171XPUF/"
}
]
},
"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/IGVFDS4103BJLT/",
"accession": "IGVFDS4103BJLT",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
],
"status": "preview"
}
],
"control_for": [],
"creation_timestamp": "2024-11-25T23:53:20.152353+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/IGVFFI2267FEGT/",
"accession": "IGVFFI2267FEGT",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T06:57:47.684946+00:00",
"file_format": "fastq",
"file_size": 9582530,
"href": "/sequence-files/IGVFFI2267FEGT/@@download/IGVFFI2267FEGT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/3fd5ba70-1dea-4865-add1-021d3caaf779/IGVFFI2267FEGT.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep1-FFrep4-BinAll-PCRrep2_S811_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6689GUPV/",
"accession": "IGVFFI6689GUPV",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T06:56:20.455219+00:00",
"file_format": "fastq",
"file_size": 10729685,
"href": "/sequence-files/IGVFFI6689GUPV/@@download/IGVFFI6689GUPV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/7f733cfe-d613-4e7f-a01e-7e3dd35ceda5/IGVFFI6689GUPV.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep1-FFrep4-BinAll-PCRrep1_S802_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8463SZQL/",
"accession": "IGVFFI8463SZQL",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T09:27:13.817750+00:00",
"file_format": "fastq",
"file_size": 11309041,
"href": "/sequence-files/IGVFFI8463SZQL/@@download/IGVFFI8463SZQL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/885c98e7-88b9-450c-8d29-f455d0b76db0/IGVFFI8463SZQL.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep1-FFrep4-BinAll-PCRrep2_S811_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6227NOXW/",
"accession": "IGVFFI6227NOXW",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T09:24:13.457293+00:00",
"file_format": "fastq",
"file_size": 12430685,
"href": "/sequence-files/IGVFFI6227NOXW/@@download/IGVFFI6227NOXW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/d21caff8-d651-4542-a3ef-538574757293/IGVFFI6227NOXW.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep1-FFrep4-BinAll-PCRrep1_S802_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4905QDDN/",
"accession": "IGVFFI4905QDDN",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T13:16:35.829792+00:00",
"file_format": "fastq",
"file_size": 4676442,
"href": "/sequence-files/IGVFFI4905QDDN/@@download/IGVFFI4905QDDN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/e1c9c9e0-2119-4519-980e-493e265fc87b/IGVFFI4905QDDN.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep1-FFrep4-BinAll-PCRrep1_S802_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9012STWQ/",
"accession": "IGVFFI9012STWQ",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T13:19:24.934280+00:00",
"file_format": "fastq",
"file_size": 4316020,
"href": "/sequence-files/IGVFFI9012STWQ/@@download/IGVFFI9012STWQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/55baebe4-6fb9-4dc3-ad1d-7d95602337bd/IGVFFI9012STWQ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep1-FFrep4-BinAll-PCRrep2_S811_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6077XTTA/",
"accession": "IGVFFI6077XTTA",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T17:13:47.305871+00:00",
"file_format": "fastq",
"file_size": 4393172,
"href": "/sequence-files/IGVFFI6077XTTA/@@download/IGVFFI6077XTTA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/3a3ffd7b-ea61-4cb2-8ab2-0fd0fd0d1ac0/IGVFFI6077XTTA.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep1-FFrep4-BinAll-PCRrep1_S802_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9485OHPE/",
"accession": "IGVFFI9485OHPE",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T17:16:46.708638+00:00",
"file_format": "fastq",
"file_size": 4080370,
"href": "/sequence-files/IGVFFI9485OHPE/@@download/IGVFFI9485OHPE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/0fe02ae1-f904-4b71-b7f0-01ed9f6bdfbd/IGVFFI9485OHPE.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep1-FFrep4-BinAll-PCRrep2_S811_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4833ZRTZ/"
],
"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/IGVFSM2428YSLH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2428YSLH",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-FACS_Input"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS4955GEYO/",
"accession": "IGVFDS4955GEYO",
"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": "2024-11-26T06:56:20.455219+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": "d7238f0b-3f70-43db-9da6-a723038a5af6"
}