{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0055JPRQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0055JPRQ",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-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 [IGVFDS0055JPRQ](/measurement-sets/IGVFDS0055JPRQ/) has sequence file(s) [IGVFFI9132PGMZ](/sequence-files/IGVFFI9132PGMZ/), [IGVFFI3771EXDX](/sequence-files/IGVFFI3771EXDX/), [IGVFFI7059LNIA](/sequence-files/IGVFFI7059LNIA/), [IGVFFI5517MYIN](/sequence-files/IGVFFI5517MYIN/), [IGVFFI0075NUXD](/sequence-files/IGVFFI0075NUXD/), [IGVFFI8950FMFU](/sequence-files/IGVFFI8950FMFU/), [IGVFFI2537GOGQ](/sequence-files/IGVFFI2537GOGQ/), [IGVFFI3359CJNQ](/sequence-files/IGVFFI3359CJNQ/) 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/IGVFDS0055JPRQ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0055JPRQ](/measurement-sets/IGVFDS0055JPRQ/) has sequence file(s): [IGVFFI9132PGMZ](/sequence-files/IGVFFI9132PGMZ/), [IGVFFI3771EXDX](/sequence-files/IGVFFI3771EXDX/), [IGVFFI7059LNIA](/sequence-files/IGVFFI7059LNIA/), [IGVFFI5517MYIN](/sequence-files/IGVFFI5517MYIN/), [IGVFFI0075NUXD](/sequence-files/IGVFFI0075NUXD/), [IGVFFI8950FMFU](/sequence-files/IGVFFI8950FMFU/), [IGVFFI2537GOGQ](/sequence-files/IGVFFI2537GOGQ/), [IGVFFI3359CJNQ](/sequence-files/IGVFFI3359CJNQ/) 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/IGVFDS0055JPRQ/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0055JPRQ](/measurement-sets/IGVFDS0055JPRQ/) 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/IGVFDS0055JPRQ/"
}
]
},
"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": "2024-12-10T22:33:57.056716+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": "IGVFFI9132PGMZ",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep2-FFrep2-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T01:35:36.049036+00:00",
"file_format": "fastq",
"file_size": 41186559,
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"s3_uri": "s3://igvf-files/2024/12/11/caf77480-3ba3-48cb-81cb-d07e08542a3d/IGVFFI9132PGMZ.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-BioRep2-FFrep2-BinAll-PCRrep1_S974_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3771EXDX/",
"accession": "IGVFFI3771EXDX",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep2-FFrep2-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T01:38:43.412189+00:00",
"file_format": "fastq",
"file_size": 43228478,
"href": "/sequence-files/IGVFFI3771EXDX/@@download/IGVFFI3771EXDX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/14853005-3cea-44f4-9203-1d37279dd7e8/IGVFFI3771EXDX.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-BioRep2-FFrep2-BinAll-PCRrep2_S986_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7059LNIA/",
"accession": "IGVFFI7059LNIA",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep2-FFrep2-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T19:36:08.199393+00:00",
"file_format": "fastq",
"file_size": 35574095,
"href": "/sequence-files/IGVFFI7059LNIA/@@download/IGVFFI7059LNIA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/b88930e4-8e9c-461c-8ff2-f0ca6e996b62/IGVFFI7059LNIA.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-BioRep2-FFrep2-BinAll-PCRrep1_S974_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5517MYIN/",
"accession": "IGVFFI5517MYIN",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep2-FFrep2-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T21:47:59.918699+00:00",
"file_format": "fastq",
"file_size": 13117417,
"href": "/sequence-files/IGVFFI5517MYIN/@@download/IGVFFI5517MYIN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/db06fcc5-f3c5-4eb7-a48d-c32e97d30130/IGVFFI5517MYIN.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-BioRep2-FFrep2-BinAll-PCRrep1_S974_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0075NUXD/",
"accession": "IGVFFI0075NUXD",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep2-FFrep2-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T21:51:03.832204+00:00",
"file_format": "fastq",
"file_size": 14512138,
"href": "/sequence-files/IGVFFI0075NUXD/@@download/IGVFFI0075NUXD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/2a731c84-5c32-4881-bab5-526bd9e35fda/IGVFFI0075NUXD.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-BioRep2-FFrep2-BinAll-PCRrep2_S986_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8950FMFU/",
"accession": "IGVFFI8950FMFU",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep2-FFrep2-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T19:39:08.837594+00:00",
"file_format": "fastq",
"file_size": 36980316,
"href": "/sequence-files/IGVFFI8950FMFU/@@download/IGVFFI8950FMFU.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/79926b61-61c3-491d-8004-fb6bc43f6a39/IGVFFI8950FMFU.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-BioRep2-FFrep2-BinAll-PCRrep2_S986_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2537GOGQ/",
"accession": "IGVFFI2537GOGQ",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep2-FFrep2-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-12T00:04:18.120615+00:00",
"file_format": "fastq",
"file_size": 13711282,
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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-BioRep2-FFrep2-BinAll-PCRrep2_S986_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3359CJNQ/",
"accession": "IGVFFI3359CJNQ",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep2-FFrep2-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
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"creation_timestamp": "2024-12-12T00:01:16.187105+00:00",
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},
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"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/IGVFSM2289HGEI/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2289HGEI",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep2-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": "2024-12-11T01:35:36.049036+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": "6c61ff71-2254-407a-9296-498ab5523017"
}