{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5266OEKB/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5266OEKB",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep3-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 [IGVFDS5266OEKB](/measurement-sets/IGVFDS5266OEKB/) has sequence file(s) [IGVFFI7280YNBF](/sequence-files/IGVFFI7280YNBF/), [IGVFFI7158ICFK](/sequence-files/IGVFFI7158ICFK/), [IGVFFI8289AMHK](/sequence-files/IGVFFI8289AMHK/), [IGVFFI0462XFML](/sequence-files/IGVFFI0462XFML/), [IGVFFI1736KRSA](/sequence-files/IGVFFI1736KRSA/), [IGVFFI2921FVWJ](/sequence-files/IGVFFI2921FVWJ/), [IGVFFI1555SXFN](/sequence-files/IGVFFI1555SXFN/), [IGVFFI9691LWUF](/sequence-files/IGVFFI9691LWUF/) 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/IGVFDS5266OEKB/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5266OEKB](/measurement-sets/IGVFDS5266OEKB/) has sequence file(s): [IGVFFI7280YNBF](/sequence-files/IGVFFI7280YNBF/), [IGVFFI7158ICFK](/sequence-files/IGVFFI7158ICFK/), [IGVFFI8289AMHK](/sequence-files/IGVFFI8289AMHK/), [IGVFFI0462XFML](/sequence-files/IGVFFI0462XFML/), [IGVFFI1736KRSA](/sequence-files/IGVFFI1736KRSA/), [IGVFFI2921FVWJ](/sequence-files/IGVFFI2921FVWJ/), [IGVFFI1555SXFN](/sequence-files/IGVFFI1555SXFN/), [IGVFFI9691LWUF](/sequence-files/IGVFFI9691LWUF/) 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/IGVFDS5266OEKB/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5266OEKB](/measurement-sets/IGVFDS5266OEKB/) 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/IGVFDS5266OEKB/"
}
]
},
"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": "2024-11-25T23:52:59.040645+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/IGVFFI7280YNBF/",
"accession": "IGVFFI7280YNBF",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep3-FACS_Input-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T06:43:20.143168+00:00",
"file_format": "fastq",
"file_size": 9483254,
"href": "/sequence-files/IGVFFI7280YNBF/@@download/IGVFFI7280YNBF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/c8fe1239-dc2e-4487-b638-632443f05ab5/IGVFFI7280YNBF.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-FFrep3-BinAll-PCRrep2_S810_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7158ICFK/",
"accession": "IGVFFI7158ICFK",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep3-FACS_Input-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T06:41:49.999060+00:00",
"file_format": "fastq",
"file_size": 9441369,
"href": "/sequence-files/IGVFFI7158ICFK/@@download/IGVFFI7158ICFK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/85efb6a3-f9f8-4b9d-be5b-2fc52992e03d/IGVFFI7158ICFK.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-FFrep3-BinAll-PCRrep1_S801_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8289AMHK/",
"accession": "IGVFFI8289AMHK",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep3-FACS_Input-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T08:58:04.493160+00:00",
"file_format": "fastq",
"file_size": 11053693,
"href": "/sequence-files/IGVFFI8289AMHK/@@download/IGVFFI8289AMHK.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/919552f0-9194-41e4-9cba-f9af5ccafaaf/IGVFFI8289AMHK.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-FFrep3-BinAll-PCRrep2_S810_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0462XFML/",
"accession": "IGVFFI0462XFML",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep3-FACS_Input-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T08:55:20.756705+00:00",
"file_format": "fastq",
"file_size": 11033671,
"href": "/sequence-files/IGVFFI0462XFML/@@download/IGVFFI0462XFML.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/2d0b77d4-c46e-490a-b3a1-61221288c2bd/IGVFFI0462XFML.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-FFrep3-BinAll-PCRrep1_S801_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1736KRSA/",
"accession": "IGVFFI1736KRSA",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep3-FACS_Input-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T12:49:57.126057+00:00",
"file_format": "fastq",
"file_size": 4228773,
"href": "/sequence-files/IGVFFI1736KRSA/@@download/IGVFFI1736KRSA.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/ad2da140-0aeb-4313-b8a6-b96d00b616b2/IGVFFI1736KRSA.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-FFrep3-BinAll-PCRrep2_S810_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2921FVWJ/",
"accession": "IGVFFI2921FVWJ",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep3-FACS_Input-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T12:47:13.419041+00:00",
"file_format": "fastq",
"file_size": 3987095,
"href": "/sequence-files/IGVFFI2921FVWJ/@@download/IGVFFI2921FVWJ.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/768a1912-17d1-4a4c-81ce-be1960e3124c/IGVFFI2921FVWJ.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-FFrep3-BinAll-PCRrep1_S801_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1555SXFN/",
"accession": "IGVFFI1555SXFN",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep3-FACS_Input-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T16:47:14.209391+00:00",
"file_format": "fastq",
"file_size": 4023760,
"href": "/sequence-files/IGVFFI1555SXFN/@@download/IGVFFI1555SXFN.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/1ce0644a-7b83-4d5c-b292-46c9290c59e7/IGVFFI1555SXFN.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-FFrep3-BinAll-PCRrep2_S810_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9691LWUF/",
"accession": "IGVFFI9691LWUF",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep3-FACS_Input-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-11-26T16:44:26.429197+00:00",
"file_format": "fastq",
"file_size": 4086867,
"href": "/sequence-files/IGVFFI9691LWUF/@@download/IGVFFI9691LWUF.fastq.gz",
"s3_uri": "s3://igvf-files/2024/11/26/5def0af7-1403-44d4-bbca-a8316980f52e/IGVFFI9691LWUF.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-FFrep3-BinAll-PCRrep1_S801_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/IGVFSM9235XIKR/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9235XIKR",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep3-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": "2024-11-26T06:41:49.999060+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": "680b25c5-b695-491c-9758-98f65c4ca98b"
}