{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9309HKUH/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9309HKUH",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-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 [IGVFDS9309HKUH](/measurement-sets/IGVFDS9309HKUH/) has sequence file(s) [IGVFFI1566DTZE](/sequence-files/IGVFFI1566DTZE/), [IGVFFI6756OTWR](/sequence-files/IGVFFI6756OTWR/), [IGVFFI9014RDKF](/sequence-files/IGVFFI9014RDKF/), [IGVFFI5743IDUY](/sequence-files/IGVFFI5743IDUY/), [IGVFFI7327KXMA](/sequence-files/IGVFFI7327KXMA/), [IGVFFI7503UMDD](/sequence-files/IGVFFI7503UMDD/), [IGVFFI1642UVRG](/sequence-files/IGVFFI1642UVRG/), [IGVFFI5597IPDK](/sequence-files/IGVFFI5597IPDK/) 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/IGVFDS9309HKUH/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS9309HKUH](/measurement-sets/IGVFDS9309HKUH/) has sequence file(s): [IGVFFI1566DTZE](/sequence-files/IGVFFI1566DTZE/), [IGVFFI6756OTWR](/sequence-files/IGVFFI6756OTWR/), [IGVFFI9014RDKF](/sequence-files/IGVFFI9014RDKF/), [IGVFFI5743IDUY](/sequence-files/IGVFFI5743IDUY/), [IGVFFI7327KXMA](/sequence-files/IGVFFI7327KXMA/), [IGVFFI7503UMDD](/sequence-files/IGVFFI7503UMDD/), [IGVFFI1642UVRG](/sequence-files/IGVFFI1642UVRG/), [IGVFFI5597IPDK](/sequence-files/IGVFFI5597IPDK/) 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/IGVFDS9309HKUH/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS9309HKUH](/measurement-sets/IGVFDS9309HKUH/) 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/IGVFDS9309HKUH/"
}
]
},
"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": "2024-11-25T23:52:41.316652+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/IGVFFI1566DTZE/",
"accession": "IGVFFI1566DTZE",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep2-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T06:27:51.196639+00:00",
"file_format": "fastq",
"file_size": 10066155,
"href": "/sequence-files/IGVFFI1566DTZE/@@download/IGVFFI1566DTZE.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/001c52e2-6a3f-475a-a55a-5e0f65c1456f/IGVFFI1566DTZE.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-BioRep1-FFrep2-BinAll-PCRrep2_S809_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6756OTWR/",
"accession": "IGVFFI6756OTWR",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep2-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T06:26:23.047985+00:00",
"file_format": "fastq",
"file_size": 10269181,
"href": "/sequence-files/IGVFFI6756OTWR/@@download/IGVFFI6756OTWR.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/ebf72840-28ba-4fbc-88ea-381417ccd2fd/IGVFFI6756OTWR.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-BioRep1-FFrep2-BinAll-PCRrep1_S800_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9014RDKF/",
"accession": "IGVFFI9014RDKF",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep2-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T08:34:30.005705+00:00",
"file_format": "fastq",
"file_size": 11530444,
"href": "/sequence-files/IGVFFI9014RDKF/@@download/IGVFFI9014RDKF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/e398aae1-8eb2-450b-8d02-f6f4080255dc/IGVFFI9014RDKF.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-BioRep1-FFrep2-BinAll-PCRrep2_S809_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5743IDUY/",
"accession": "IGVFFI5743IDUY",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep2-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T08:32:30.647981+00:00",
"file_format": "fastq",
"file_size": 11901920,
"href": "/sequence-files/IGVFFI5743IDUY/@@download/IGVFFI5743IDUY.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/49464906-c449-4908-856d-970ae9ba1a0b/IGVFFI5743IDUY.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-BioRep1-FFrep2-BinAll-PCRrep1_S800_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7327KXMA/",
"accession": "IGVFFI7327KXMA",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep2-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T12:18:53.201440+00:00",
"file_format": "fastq",
"file_size": 4289741,
"href": "/sequence-files/IGVFFI7327KXMA/@@download/IGVFFI7327KXMA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/2b189cdf-3bea-4ebb-84c5-4f3996982b79/IGVFFI7327KXMA.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-BioRep1-FFrep2-BinAll-PCRrep1_S800_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7503UMDD/",
"accession": "IGVFFI7503UMDD",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep2-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T12:21:46.423999+00:00",
"file_format": "fastq",
"file_size": 4311574,
"href": "/sequence-files/IGVFFI7503UMDD/@@download/IGVFFI7503UMDD.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/cf6aff80-c156-4635-beaa-cc9b06826f2b/IGVFFI7503UMDD.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-BioRep1-FFrep2-BinAll-PCRrep2_S809_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1642UVRG/",
"accession": "IGVFFI1642UVRG",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep2-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T16:17:27.381771+00:00",
"file_format": "fastq",
"file_size": 4436800,
"href": "/sequence-files/IGVFFI1642UVRG/@@download/IGVFFI1642UVRG.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/05afd1dc-6826-4574-8814-efd416255f6c/IGVFFI1642UVRG.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-BioRep1-FFrep2-BinAll-PCRrep2_S809_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5597IPDK/",
"accession": "IGVFFI5597IPDK",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep2-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T16:14:30.932669+00:00",
"file_format": "fastq",
"file_size": 4370325,
"href": "/sequence-files/IGVFFI5597IPDK/@@download/IGVFFI5597IPDK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/720e9025-a22f-4bee-8063-3d5319575fb9/IGVFFI5597IPDK.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep1-FFrep2-BinAll-PCRrep1_S800_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/IGVFSM5578CHGC/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5578CHGC",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep2-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": "2024-11-26T06:26:23.047985+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": "be0b7cde-1d56-495f-84e5-ce74d88a7849"
}