{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4310WOQM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4310WOQM",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep1-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 [IGVFDS4310WOQM](/measurement-sets/IGVFDS4310WOQM/) has sequence file(s) [IGVFFI2551MBUE](/sequence-files/IGVFFI2551MBUE/), [IGVFFI3771GJUQ](/sequence-files/IGVFFI3771GJUQ/), [IGVFFI5442CVUH](/sequence-files/IGVFFI5442CVUH/), [IGVFFI4596MWER](/sequence-files/IGVFFI4596MWER/), [IGVFFI7964YXUR](/sequence-files/IGVFFI7964YXUR/), [IGVFFI0730WYAI](/sequence-files/IGVFFI0730WYAI/), [IGVFFI5760KHNI](/sequence-files/IGVFFI5760KHNI/), [IGVFFI8794RMUN](/sequence-files/IGVFFI8794RMUN/) 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/IGVFDS4310WOQM/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4310WOQM](/measurement-sets/IGVFDS4310WOQM/) has sequence file(s): [IGVFFI2551MBUE](/sequence-files/IGVFFI2551MBUE/), [IGVFFI3771GJUQ](/sequence-files/IGVFFI3771GJUQ/), [IGVFFI5442CVUH](/sequence-files/IGVFFI5442CVUH/), [IGVFFI4596MWER](/sequence-files/IGVFFI4596MWER/), [IGVFFI7964YXUR](/sequence-files/IGVFFI7964YXUR/), [IGVFFI0730WYAI](/sequence-files/IGVFFI0730WYAI/), [IGVFFI5760KHNI](/sequence-files/IGVFFI5760KHNI/), [IGVFFI8794RMUN](/sequence-files/IGVFFI8794RMUN/) 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/IGVFDS4310WOQM/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4310WOQM](/measurement-sets/IGVFDS4310WOQM/) 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/IGVFDS4310WOQM/"
}
]
},
"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": "2024-12-10T22:32:43.148094+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": [
{
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"accession": "IGVFFI2551MBUE",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep1-FFrep2-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T00:46:48.404933+00:00",
"file_format": "fastq",
"file_size": 33422362,
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"s3_uri": "s3://igvf-files/2024/12/11/e24ec1c6-3893-4f1c-ba66-e9af8aa7b869/IGVFFI2551MBUE.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C11-Amp_PPIF_5splicesite-BioRep1-FFrep2-BinAll-PCRrep2_S984_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3771GJUQ/",
"accession": "IGVFFI3771GJUQ",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep1-FFrep2-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T00:43:44.337567+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI3771GJUQ/@@download/IGVFFI3771GJUQ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/9dbfa043-3dd0-4082-95ee-7907d48fa28f/IGVFFI3771GJUQ.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_C11-Amp_PPIF_5splicesite-BioRep1-FFrep2-BinAll-PCRrep1_S972_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5442CVUH/",
"accession": "IGVFFI5442CVUH",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep1-FFrep2-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T17:31:56.690451+00:00",
"file_format": "fastq",
"file_size": 36110946,
"href": "/sequence-files/IGVFFI5442CVUH/@@download/IGVFFI5442CVUH.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/d7b8d808-0707-4610-9ba8-f8bb131f3d40/IGVFFI5442CVUH.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_C11-Amp_PPIF_5splicesite-BioRep1-FFrep2-BinAll-PCRrep1_S972_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4596MWER/",
"accession": "IGVFFI4596MWER",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep1-FFrep2-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T17:34:34.488065+00:00",
"file_format": "fastq",
"file_size": 29639192,
"href": "/sequence-files/IGVFFI4596MWER/@@download/IGVFFI4596MWER.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/90a8789a-f605-4876-8d08-bbfb3a147d4a/IGVFFI4596MWER.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_C11-Amp_PPIF_5splicesite-BioRep1-FFrep2-BinAll-PCRrep2_S984_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7964YXUR/",
"accession": "IGVFFI7964YXUR",
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"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep1-FFrep2-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T21:25:37.431466+00:00",
"file_format": "fastq",
"file_size": 14011060,
"href": "/sequence-files/IGVFFI7964YXUR/@@download/IGVFFI7964YXUR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/c7228ee5-7796-420b-94ff-239b947a6492/IGVFFI7964YXUR.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C11-Amp_PPIF_5splicesite-BioRep1-FFrep2-BinAll-PCRrep1_S972_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0730WYAI/",
"accession": "IGVFFI0730WYAI",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep1-FFrep2-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T21:28:37.290488+00:00",
"file_format": "fastq",
"file_size": 12945048,
"href": "/sequence-files/IGVFFI0730WYAI/@@download/IGVFFI0730WYAI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/8703eb85-5464-4789-862a-4bad44dc5ccd/IGVFFI0730WYAI.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C11-Amp_PPIF_5splicesite-BioRep1-FFrep2-BinAll-PCRrep2_S984_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5760KHNI/",
"accession": "IGVFFI5760KHNI",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep1-FFrep2-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T23:38:22.719504+00:00",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C11-Amp_PPIF_5splicesite-BioRep1-FFrep2-BinAll-PCRrep1_S972_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8794RMUN/",
"accession": "IGVFFI8794RMUN",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep1-FFrep2-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T23:41:32.808228+00:00",
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
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"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C11-Amp_PPIF_5splicesite-BioRep1-FFrep2-BinAll-PCRrep2_S984_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1132MKHT/"
],
"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/IGVFSM3742TXQB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3742TXQB",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep1-FFrep2-FACS_Input"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS2432IDGC/",
"accession": "IGVFDS2432IDGC",
"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": "2024-12-11T00:43:44.337567+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": "d8c3d491-ccfe-4da7-94fa-93ce947323e2"
}