{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2754BSGV/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2754BSGV",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCAG-THP1-BioRep2-FFrep2-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 [IGVFDS2754BSGV](/measurement-sets/IGVFDS2754BSGV/) has sequence file(s) [IGVFFI4425QHKS](/sequence-files/IGVFFI4425QHKS/), [IGVFFI1128WKYC](/sequence-files/IGVFFI1128WKYC/), [IGVFFI5379RAXM](/sequence-files/IGVFFI5379RAXM/), [IGVFFI5934WCBS](/sequence-files/IGVFFI5934WCBS/), [IGVFFI4477YRNN](/sequence-files/IGVFFI4477YRNN/), [IGVFFI5715EAKZ](/sequence-files/IGVFFI5715EAKZ/), [IGVFFI2102GQAY](/sequence-files/IGVFFI2102GQAY/), [IGVFFI7932FFGQ](/sequence-files/IGVFFI7932FFGQ/) 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/IGVFDS2754BSGV/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2754BSGV](/measurement-sets/IGVFDS2754BSGV/) has sequence file(s): [IGVFFI4425QHKS](/sequence-files/IGVFFI4425QHKS/), [IGVFFI1128WKYC](/sequence-files/IGVFFI1128WKYC/), [IGVFFI5379RAXM](/sequence-files/IGVFFI5379RAXM/), [IGVFFI5934WCBS](/sequence-files/IGVFFI5934WCBS/), [IGVFFI4477YRNN](/sequence-files/IGVFFI4477YRNN/), [IGVFFI5715EAKZ](/sequence-files/IGVFFI5715EAKZ/), [IGVFFI2102GQAY](/sequence-files/IGVFFI2102GQAY/), [IGVFFI7932FFGQ](/sequence-files/IGVFFI7932FFGQ/) 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/IGVFDS2754BSGV/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2754BSGV](/measurement-sets/IGVFDS2754BSGV/) 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/IGVFDS2754BSGV/"
}
]
},
"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/IGVFDS8210FQOO/",
"accession": "IGVFDS8210FQOO",
"aliases": [
"jesse-engreitz:THP1-PE2_Exp7_PPIF_5SpliceSite-IndividualVariantExp_NegControl_AmpliconSequencing"
],
"status": "preview"
}
],
"control_for": [],
"creation_timestamp": "2024-12-10T22:36:38.435886+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/IGVFFI4425QHKS/",
"accession": "IGVFFI4425QHKS",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCAG-THP1-BioRep2-FFrep2-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T16:52:04.422571+00:00",
"file_format": "fastq",
"file_size": 41489329,
"href": "/sequence-files/IGVFFI4425QHKS/@@download/IGVFFI4425QHKS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/0eece803-45ab-4d97-afa7-9e556129bacb/IGVFFI4425QHKS.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_C12-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinAll-PCRrep2_S996_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1128WKYC/",
"accession": "IGVFFI1128WKYC",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCAG-THP1-BioRep2-FFrep2-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T16:50:33.744197+00:00",
"file_format": "fastq",
"file_size": 35779339,
"href": "/sequence-files/IGVFFI1128WKYC/@@download/IGVFFI1128WKYC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/9a5939cf-44a8-414c-9d3f-e09c9e9cafc5/IGVFFI1128WKYC.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_C12-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinAll-PCRrep1_S990_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5379RAXM/",
"accession": "IGVFFI5379RAXM",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCAG-THP1-BioRep2-FFrep2-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T20:22:52.042931+00:00",
"file_format": "fastq",
"file_size": 35640130,
"href": "/sequence-files/IGVFFI5379RAXM/@@download/IGVFFI5379RAXM.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/8557778d-f772-416f-96c2-1b7732718be1/IGVFFI5379RAXM.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_C12-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinAll-PCRrep2_S996_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5934WCBS/",
"accession": "IGVFFI5934WCBS",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCAG-THP1-BioRep2-FFrep2-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T20:19:58.444999+00:00",
"file_format": "fastq",
"file_size": 31547650,
"href": "/sequence-files/IGVFFI5934WCBS/@@download/IGVFFI5934WCBS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/cb0d6bca-533a-4078-a084-95c967e47383/IGVFFI5934WCBS.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_C12-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinAll-PCRrep1_S990_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4477YRNN/",
"accession": "IGVFFI4477YRNN",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCAG-THP1-BioRep2-FFrep2-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T22:35:27.461736+00:00",
"file_format": "fastq",
"file_size": 14311789,
"href": "/sequence-files/IGVFFI4477YRNN/@@download/IGVFFI4477YRNN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/69a5ee1a-8e13-462c-8753-1fe6b37f8b87/IGVFFI4477YRNN.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_C12-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinAll-PCRrep2_S996_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5715EAKZ/",
"accession": "IGVFFI5715EAKZ",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCAG-THP1-BioRep2-FFrep2-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-12T00:46:14.223335+00:00",
"file_format": "fastq",
"file_size": 11815005,
"href": "/sequence-files/IGVFFI5715EAKZ/@@download/IGVFFI5715EAKZ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/12/179eb352-91db-40a4-958c-15864955f4b6/IGVFFI5715EAKZ.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_C12-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinAll-PCRrep1_S990_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2102GQAY/",
"accession": "IGVFFI2102GQAY",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCAG-THP1-BioRep2-FFrep2-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T22:32:25.969235+00:00",
"file_format": "fastq",
"file_size": 12526154,
"href": "/sequence-files/IGVFFI2102GQAY/@@download/IGVFFI2102GQAY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/a488349c-1446-475f-8487-784d33322761/IGVFFI2102GQAY.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_C12-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinAll-PCRrep1_S990_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7932FFGQ/",
"accession": "IGVFFI7932FFGQ",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCAG-THP1-BioRep2-FFrep2-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-12T00:49:21.391981+00:00",
"file_format": "fastq",
"file_size": 13545388,
"href": "/sequence-files/IGVFFI7932FFGQ/@@download/IGVFFI7932FFGQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/12/d88bd555-4c25-4243-add7-d19c2fee9945/IGVFFI7932FFGQ.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_C12-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinAll-PCRrep2_S996_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS8174BPPS/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"preferred_assay_title": "Variant-EFFECTS",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8027FBQH/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8027FBQH",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCAG-THP1-BioRep2-FFrep2-FACS_Input"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6555EOZU/",
"accession": "IGVFDS6555EOZU",
"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": "2024-12-11T16:50:33.744197+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": "2c4ba9cd-0dc9-4ce9-b38b-7b51fedee17b"
}