{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0958ZMWD/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0958ZMWD",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep4-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 [IGVFDS0958ZMWD](/measurement-sets/IGVFDS0958ZMWD/) has sequence file(s) [IGVFFI6577PXWB](/sequence-files/IGVFFI6577PXWB/), [IGVFFI5542SKQI](/sequence-files/IGVFFI5542SKQI/), [IGVFFI1327ALTG](/sequence-files/IGVFFI1327ALTG/), [IGVFFI3455BXOP](/sequence-files/IGVFFI3455BXOP/), [IGVFFI6723ELCL](/sequence-files/IGVFFI6723ELCL/), [IGVFFI5103PMSC](/sequence-files/IGVFFI5103PMSC/), [IGVFFI9584LEOX](/sequence-files/IGVFFI9584LEOX/), [IGVFFI8527QSHR](/sequence-files/IGVFFI8527QSHR/) 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/IGVFDS0958ZMWD/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0958ZMWD](/measurement-sets/IGVFDS0958ZMWD/) has sequence file(s): [IGVFFI6577PXWB](/sequence-files/IGVFFI6577PXWB/), [IGVFFI5542SKQI](/sequence-files/IGVFFI5542SKQI/), [IGVFFI1327ALTG](/sequence-files/IGVFFI1327ALTG/), [IGVFFI3455BXOP](/sequence-files/IGVFFI3455BXOP/), [IGVFFI6723ELCL](/sequence-files/IGVFFI6723ELCL/), [IGVFFI5103PMSC](/sequence-files/IGVFFI5103PMSC/), [IGVFFI9584LEOX](/sequence-files/IGVFFI9584LEOX/), [IGVFFI8527QSHR](/sequence-files/IGVFFI8527QSHR/) 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/IGVFDS0958ZMWD/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0958ZMWD](/measurement-sets/IGVFDS0958ZMWD/) 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/IGVFDS0958ZMWD/"
}
]
},
"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/IGVFDS4103BJLT/",
"accession": "IGVFDS4103BJLT",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
],
"status": "preview"
}
],
"control_for": [],
"creation_timestamp": "2024-11-25T23:54:47.098543+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": [
{
"@id": "/sequence-files/IGVFFI6577PXWB/",
"accession": "IGVFFI6577PXWB",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep4-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T07:57:47.004850+00:00",
"file_format": "fastq",
"file_size": 10655757,
"href": "/sequence-files/IGVFFI6577PXWB/@@download/IGVFFI6577PXWB.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/856d9299-f273-4257-ab4b-0e87fa012e0b/IGVFFI6577PXWB.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep2-FFrep4-BinAll-PCRrep1_S806_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5542SKQI/",
"accession": "IGVFFI5542SKQI",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep4-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T07:59:23.285994+00:00",
"file_format": "fastq",
"file_size": 10910100,
"href": "/sequence-files/IGVFFI5542SKQI/@@download/IGVFFI5542SKQI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/ba204b63-6913-4e1d-b5b8-0fbc0e61b48b/IGVFFI5542SKQI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep2-FFrep4-BinAll-PCRrep2_S815_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1327ALTG/",
"accession": "IGVFFI1327ALTG",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep4-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T11:22:38.671754+00:00",
"file_format": "fastq",
"file_size": 12663890,
"href": "/sequence-files/IGVFFI1327ALTG/@@download/IGVFFI1327ALTG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/5eaad445-5b41-4828-b993-a233d466f0fc/IGVFFI1327ALTG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep2-FFrep4-BinAll-PCRrep2_S815_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3455BXOP/",
"accession": "IGVFFI3455BXOP",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep4-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T11:19:46.062074+00:00",
"file_format": "fastq",
"file_size": 12367700,
"href": "/sequence-files/IGVFFI3455BXOP/@@download/IGVFFI3455BXOP.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/9a400258-be9d-4d0c-ac17-f9b5a0c65c4b/IGVFFI3455BXOP.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep2-FFrep4-BinAll-PCRrep1_S806_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6723ELCL/",
"accession": "IGVFFI6723ELCL",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep4-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T15:16:59.318939+00:00",
"file_format": "fastq",
"file_size": 4630670,
"href": "/sequence-files/IGVFFI6723ELCL/@@download/IGVFFI6723ELCL.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/7c7c32fb-fe7e-4e91-8ae3-9edf7bb94b64/IGVFFI6723ELCL.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep2-FFrep4-BinAll-PCRrep2_S815_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5103PMSC/",
"accession": "IGVFFI5103PMSC",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep4-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T15:14:06.633098+00:00",
"file_format": "fastq",
"file_size": 4471489,
"href": "/sequence-files/IGVFFI5103PMSC/@@download/IGVFFI5103PMSC.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/c660ea23-52ba-4874-93b3-bda53a7149c6/IGVFFI5103PMSC.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep2-FFrep4-BinAll-PCRrep1_S806_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9584LEOX/",
"accession": "IGVFFI9584LEOX",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep4-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T19:12:50.921827+00:00",
"file_format": "fastq",
"file_size": 4504024,
"href": "/sequence-files/IGVFFI9584LEOX/@@download/IGVFFI9584LEOX.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/1e7c8e47-8110-45d4-9194-b61bec03794a/IGVFFI9584LEOX.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep2-FFrep4-BinAll-PCRrep1_S806_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8527QSHR/",
"accession": "IGVFFI8527QSHR",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep4-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T19:15:44.760403+00:00",
"file_format": "fastq",
"file_size": 4800479,
"href": "/sequence-files/IGVFFI8527QSHR/@@download/IGVFFI8527QSHR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/4f4238e5-c0b8-44f0-9985-a9f8b56ff1a2/IGVFFI8527QSHR.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep2-FFrep4-BinAll-PCRrep2_S815_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4833ZRTZ/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "This measurement set previously used Variant FlowFISH as a preferred_assay_title, but this enum is now removed. So it has been defaulted to Variant-EFFECTS.",
"preferred_assay_title": "Variant-EFFECTS",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2515ITJE/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2515ITJE",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep4-FACS_Input"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS4955GEYO/",
"accession": "IGVFDS4955GEYO",
"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": "2024-11-26T07:57:47.004850+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": "511f94e5-3ef3-4821-9f42-e2a84bfac406"
}