{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5663OZRS/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5663OZRS",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCAG-THP1-BioRep2-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 [IGVFDS5663OZRS](/measurement-sets/IGVFDS5663OZRS/) has sequence file(s) [IGVFFI5857YHXZ](/sequence-files/IGVFFI5857YHXZ/), [IGVFFI9771GKYS](/sequence-files/IGVFFI9771GKYS/), [IGVFFI4023MDMW](/sequence-files/IGVFFI4023MDMW/), [IGVFFI4234OCHB](/sequence-files/IGVFFI4234OCHB/), [IGVFFI4262NLYB](/sequence-files/IGVFFI4262NLYB/), [IGVFFI0873NVGX](/sequence-files/IGVFFI0873NVGX/), [IGVFFI2113UGIX](/sequence-files/IGVFFI2113UGIX/), [IGVFFI0141VVXE](/sequence-files/IGVFFI0141VVXE/) 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/IGVFDS5663OZRS/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5663OZRS](/measurement-sets/IGVFDS5663OZRS/) has sequence file(s): [IGVFFI5857YHXZ](/sequence-files/IGVFFI5857YHXZ/), [IGVFFI9771GKYS](/sequence-files/IGVFFI9771GKYS/), [IGVFFI4023MDMW](/sequence-files/IGVFFI4023MDMW/), [IGVFFI4234OCHB](/sequence-files/IGVFFI4234OCHB/), [IGVFFI4262NLYB](/sequence-files/IGVFFI4262NLYB/), [IGVFFI0873NVGX](/sequence-files/IGVFFI0873NVGX/), [IGVFFI2113UGIX](/sequence-files/IGVFFI2113UGIX/), [IGVFFI0141VVXE](/sequence-files/IGVFFI0141VVXE/) 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/IGVFDS5663OZRS/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5663OZRS](/measurement-sets/IGVFDS5663OZRS/) 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/IGVFDS5663OZRS/"
}
]
},
"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": "2024-12-10T22:35:52.956151+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": "IGVFFI5857YHXZ",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T16:45:05.735116+00:00",
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"file_size": 40352844,
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9771GKYS/",
"accession": "IGVFFI9771GKYS",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCAG-THP1-BioRep2-FFrep1-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T16:46:37.306126+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI9771GKYS/@@download/IGVFFI9771GKYS.fastq.gz",
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"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-FFrep1-BinAll-PCRrep2_S995_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4023MDMW/",
"accession": "IGVFFI4023MDMW",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCAG-THP1-BioRep2-FFrep1-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T20:11:57.395536+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI4023MDMW/@@download/IGVFFI4023MDMW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/2386b27a-6d29-423b-9d9b-690b712a0281/IGVFFI4023MDMW.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-FFrep1-BinAll-PCRrep2_S995_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4234OCHB/",
"accession": "IGVFFI4234OCHB",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCAG-THP1-BioRep2-FFrep1-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T20:08:51.782786+00:00",
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"file_size": 35059451,
"href": "/sequence-files/IGVFFI4234OCHB/@@download/IGVFFI4234OCHB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/4a5b1e90-1cc7-4d6f-a3e9-30e212cb6e99/IGVFFI4234OCHB.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-FFrep1-BinAll-PCRrep1_S989_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4262NLYB/",
"accession": "IGVFFI4262NLYB",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCAG-THP1-BioRep2-FFrep1-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T22:24:19.915409+00:00",
"file_format": "fastq",
"file_size": 15286417,
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"s3_uri": "s3://igvf-files/2024/12/11/5cb931c9-29e7-43c4-9507-68e2ed149cc3/IGVFFI4262NLYB.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_C12-Amp_PPIF_5splicesite-BioRep2-FFrep1-BinAll-PCRrep2_S995_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0873NVGX/",
"accession": "IGVFFI0873NVGX",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCAG-THP1-BioRep2-FFrep1-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-12T00:35:20.051861+00:00",
"file_format": "fastq",
"file_size": 13166035,
"href": "/sequence-files/IGVFFI0873NVGX/@@download/IGVFFI0873NVGX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/12/7450ebfa-2064-49f4-9e62-a8048d5de261/IGVFFI0873NVGX.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_C12-Amp_PPIF_5splicesite-BioRep2-FFrep1-BinAll-PCRrep1_S989_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2113UGIX/",
"accession": "IGVFFI2113UGIX",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCAG-THP1-BioRep2-FFrep1-FACS_Input-PCRrep1_I1"
],
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"creation_timestamp": "2024-12-11T22:21:13.090790+00:00",
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C12-Amp_PPIF_5splicesite-BioRep2-FFrep1-BinAll-PCRrep1_S989_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0141VVXE/",
"accession": "IGVFFI0141VVXE",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCAG-THP1-BioRep2-FFrep1-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-12T00:38:28.019407+00:00",
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"status": "released",
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},
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"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/IGVFSM4533NOSQ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4533NOSQ",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCAG-THP1-BioRep2-FFrep1-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": "2024-12-11T16:45:05.735116+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": "b243ce5b-54e7-4bfa-9e7c-0c2ae82cdb6b"
}