{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3793UEHT/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3793UEHT",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep1-FACS_Input_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"assay_slims": [
"CRISPR screens"
],
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS3793UEHT](/measurement-sets/IGVFDS3793UEHT/) has sequence file(s) [IGVFFI9820ZBNI](/sequence-files/IGVFFI9820ZBNI/), [IGVFFI7451YGJF](/sequence-files/IGVFFI7451YGJF/), [IGVFFI7205ODIS](/sequence-files/IGVFFI7205ODIS/), [IGVFFI9120SEWL](/sequence-files/IGVFFI9120SEWL/), [IGVFFI9296NSBS](/sequence-files/IGVFFI9296NSBS/), [IGVFFI8974BICU](/sequence-files/IGVFFI8974BICU/), [IGVFFI1897CJVK](/sequence-files/IGVFFI1897CJVK/), [IGVFFI0412UONO](/sequence-files/IGVFFI0412UONO/) which lack specification of a `sequencing_kit`. Sequence files in a file set associated wtih bulk data should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS3793UEHT/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3793UEHT](/measurement-sets/IGVFDS3793UEHT/) has sequence file(s): [IGVFFI9820ZBNI](/sequence-files/IGVFFI9820ZBNI/), [IGVFFI7451YGJF](/sequence-files/IGVFFI7451YGJF/), [IGVFFI7205ODIS](/sequence-files/IGVFFI7205ODIS/), [IGVFFI9120SEWL](/sequence-files/IGVFFI9120SEWL/), [IGVFFI9296NSBS](/sequence-files/IGVFFI9296NSBS/), [IGVFFI8974BICU](/sequence-files/IGVFFI8974BICU/), [IGVFFI1897CJVK](/sequence-files/IGVFFI1897CJVK/), [IGVFFI0412UONO](/sequence-files/IGVFFI0412UONO/) which do not have any `seqspecs`. Sequence files in a file set associated with bulk data are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS3793UEHT/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS3793UEHT](/measurement-sets/IGVFDS3793UEHT/) 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/IGVFDS3793UEHT/"
}
]
},
"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"
},
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS9097TEUZ/",
"accession": "IGVFDS9097TEUZ",
"file_set_type": "guide library",
"status": "preview",
"summary": "guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"control_file_sets": [
{
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"accession": "IGVFDS8210FQOO",
"aliases": [
"jesse-engreitz:THP1-PE2_Exp7_PPIF_5SpliceSite-IndividualVariantExp_NegControl_AmpliconSequencing"
],
"status": "preview"
}
],
"control_for": [],
"creation_timestamp": "2024-12-10T22:39:15.482988+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",
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{
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"accession": "IGVFFI9820ZBNI",
"aliases": [
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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/IGVFFI7451YGJF/",
"accession": "IGVFFI7451YGJF",
"aliases": [
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"controlled_access": false,
"creation_timestamp": "2024-12-11T00:10:27.515209+00:00",
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"href": "/sequence-files/IGVFFI7451YGJF/@@download/IGVFFI7451YGJF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/6b7a6c13-60ce-4da0-be29-07bf9c2229f9/IGVFFI7451YGJF.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_C10-Amp_PPIF_5splicesite-BioRep2-FFrep1-BinAll-PCRrep1_S969_R1_001.fastq.gz",
"upload_status": "validated"
},
{
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"accession": "IGVFFI7205ODIS",
"aliases": [
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],
"content_type": "reads",
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"file_format": "fastq",
"file_size": 32580380,
"href": "/sequence-files/IGVFFI7205ODIS/@@download/IGVFFI7205ODIS.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/c2c01ac0-e873-4524-9f85-5859136e3656/IGVFFI7205ODIS.fastq.gz",
"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/IGVFFI9120SEWL/",
"accession": "IGVFFI9120SEWL",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep1-FACS_Input-PCRrep2_R2"
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"creation_timestamp": "2024-12-11T17:10:20.727241+00:00",
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"s3_uri": "s3://igvf-files/2024/12/11/46407ebf-cf23-4802-93dc-fa5d7cc24bea/IGVFFI9120SEWL.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
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},
{
"@id": "/sequence-files/IGVFFI9296NSBS/",
"accession": "IGVFFI9296NSBS",
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],
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
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},
{
"@id": "/sequence-files/IGVFFI8974BICU/",
"accession": "IGVFFI8974BICU",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep1-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T20:52:33.872427+00:00",
"file_format": "fastq",
"file_size": 12767615,
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"s3_uri": "s3://igvf-files/2024/12/11/d7cb2f12-19d0-4688-98be-1cbbaaa6eb4f/IGVFFI8974BICU.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1897CJVK/",
"accession": "IGVFFI1897CJVK",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep1-FACS_Input-PCRrep1_I2"
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"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T23:05:37.570718+00:00",
"file_format": "fastq",
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"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep2-FFrep1-BinAll-PCRrep1_S969_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0412UONO/",
"accession": "IGVFFI0412UONO",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep1-FACS_Input-PCRrep2_I2"
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"content_type": "reads",
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"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep2-FFrep1-BinAll-PCRrep2_S981_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS8267JJHO/"
],
"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/IGVFSM1529SCAD/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1529SCAD",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep1-FACS_Input"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"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": "Homo sapiens (male) THP-1 cell line modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "preview",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2024-12-11T00:10:27.515209+00:00",
"summary": "CRISPR prime editing Variant-EFFECTS sorted on the expression of PPIF 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": [
"PPIase F",
"peptidylprolyl isomerase F",
"Cyp-D",
"peptidyl-prolyl cis-trans isomerase F, mitochondrial",
"PPIF",
"CyP-M",
"cyclophilin F",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"cyclophilin 3",
"cyclophilin D",
"rotamase F",
"mitochondrial cyclophilin",
"CypD",
"CYP3"
]
}
],
"uuid": "cc91c1d6-717e-473f-b9e6-a44c083f1cb2"
}