{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2821SYCZ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2821SYCZ",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-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 [IGVFDS2821SYCZ](/measurement-sets/IGVFDS2821SYCZ/) has sequence file(s) [IGVFFI2540CSBV](/sequence-files/IGVFFI2540CSBV/), [IGVFFI8245CWHJ](/sequence-files/IGVFFI8245CWHJ/), [IGVFFI0770GBZI](/sequence-files/IGVFFI0770GBZI/), [IGVFFI2294HIIW](/sequence-files/IGVFFI2294HIIW/), [IGVFFI0730QGFV](/sequence-files/IGVFFI0730QGFV/), [IGVFFI6419WVIT](/sequence-files/IGVFFI6419WVIT/), [IGVFFI5327LCXF](/sequence-files/IGVFFI5327LCXF/), [IGVFFI9293PXFB](/sequence-files/IGVFFI9293PXFB/) 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/IGVFDS2821SYCZ/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2821SYCZ](/measurement-sets/IGVFDS2821SYCZ/) has sequence file(s): [IGVFFI2540CSBV](/sequence-files/IGVFFI2540CSBV/), [IGVFFI8245CWHJ](/sequence-files/IGVFFI8245CWHJ/), [IGVFFI0770GBZI](/sequence-files/IGVFFI0770GBZI/), [IGVFFI2294HIIW](/sequence-files/IGVFFI2294HIIW/), [IGVFFI0730QGFV](/sequence-files/IGVFFI0730QGFV/), [IGVFFI6419WVIT](/sequence-files/IGVFFI6419WVIT/), [IGVFFI5327LCXF](/sequence-files/IGVFFI5327LCXF/), [IGVFFI9293PXFB](/sequence-files/IGVFFI9293PXFB/) 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/IGVFDS2821SYCZ/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2821SYCZ](/measurement-sets/IGVFDS2821SYCZ/) 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/IGVFDS2821SYCZ/"
}
]
},
"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": "2024-12-10T22:39:52.857977+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": "IGVFFI2540CSBV",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T00:24:19.116365+00:00",
"file_format": "fastq",
"file_size": 38509272,
"href": "/sequence-files/IGVFFI2540CSBV/@@download/IGVFFI2540CSBV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/bf0ead31-1f97-42b4-abbc-fe0218dd29ca/IGVFFI2540CSBV.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_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinAll-PCRrep2_S982_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8245CWHJ/",
"accession": "IGVFFI8245CWHJ",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T00:21:10.634997+00:00",
"file_format": "fastq",
"file_size": 36133716,
"href": "/sequence-files/IGVFFI8245CWHJ/@@download/IGVFFI8245CWHJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/e5467d7e-5e4d-403d-be9a-d18fd75def11/IGVFFI8245CWHJ.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-FFrep2-BinAll-PCRrep1_S970_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0770GBZI/",
"accession": "IGVFFI0770GBZI",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T17:15:26.654609+00:00",
"file_format": "fastq",
"file_size": 31255932,
"href": "/sequence-files/IGVFFI0770GBZI/@@download/IGVFFI0770GBZI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/d939d291-d0d4-4ec5-970d-1203a76578f2/IGVFFI0770GBZI.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-FFrep2-BinAll-PCRrep1_S970_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2294HIIW/",
"accession": "IGVFFI2294HIIW",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T17:17:28.857564+00:00",
"file_format": "fastq",
"file_size": 33043960,
"href": "/sequence-files/IGVFFI2294HIIW/@@download/IGVFFI2294HIIW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/063f2896-e869-4340-bab4-4c80f81af36d/IGVFFI2294HIIW.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-FFrep2-BinAll-PCRrep2_S982_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0730QGFV/",
"accession": "IGVFFI0730QGFV",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T21:06:49.684131+00:00",
"file_format": "fastq",
"file_size": 13071098,
"href": "/sequence-files/IGVFFI0730QGFV/@@download/IGVFFI0730QGFV.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/c2468792-8644-470c-ab71-873c7043ebb5/IGVFFI0730QGFV.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-FFrep2-BinAll-PCRrep2_S982_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6419WVIT/",
"accession": "IGVFFI6419WVIT",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T23:16:34.747392+00:00",
"file_format": "fastq",
"file_size": 11686047,
"href": "/sequence-files/IGVFFI6419WVIT/@@download/IGVFFI6419WVIT.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/29866c64-ed6a-4575-ac56-468fa64cf0cc/IGVFFI6419WVIT.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-FFrep2-BinAll-PCRrep1_S970_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5327LCXF/",
"accession": "IGVFFI5327LCXF",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T21:03:46.043595+00:00",
"file_format": "fastq",
"file_size": 12191597,
"href": "/sequence-files/IGVFFI5327LCXF/@@download/IGVFFI5327LCXF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/c862796e-ab55-4a6b-a22c-8e1c27f7ceb6/IGVFFI5327LCXF.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_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinAll-PCRrep1_S970_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9293PXFB/",
"accession": "IGVFFI9293PXFB",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-11T23:19:32.967730+00:00",
"file_format": "fastq",
"file_size": 12184985,
"href": "/sequence-files/IGVFFI9293PXFB/@@download/IGVFFI9293PXFB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/12/11/98484bf9-81e8-4e52-bcb5-2273881a1ddd/IGVFFI9293PXFB.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_C10-Amp_PPIF_5splicesite-BioRep2-FFrep2-BinAll-PCRrep2_S982_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/IGVFSM3128BTFC/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3128BTFC",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep2-FFrep2-FACS_Input"
],
"classifications": [
"cell line"
],
"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"
}
],
"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": "2024-12-11T00:21:10.634997+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": "489a2062-0c35-4851-a9df-88a2f43d3d08"
}