{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5064DHZL/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5064DHZL",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinF_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 [IGVFDS5064DHZL](/measurement-sets/IGVFDS5064DHZL/) has sequence file(s) [IGVFFI5444WATG](/sequence-files/IGVFFI5444WATG/), [IGVFFI1802NEVC](/sequence-files/IGVFFI1802NEVC/), [IGVFFI3327ITFG](/sequence-files/IGVFFI3327ITFG/), [IGVFFI1073RXEY](/sequence-files/IGVFFI1073RXEY/), [IGVFFI2427MOBZ](/sequence-files/IGVFFI2427MOBZ/), [IGVFFI8568QRZX](/sequence-files/IGVFFI8568QRZX/), [IGVFFI5194YEQC](/sequence-files/IGVFFI5194YEQC/), [IGVFFI7864OIDV](/sequence-files/IGVFFI7864OIDV/) 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/IGVFDS5064DHZL/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5064DHZL](/measurement-sets/IGVFDS5064DHZL/) has sequence file(s): [IGVFFI5444WATG](/sequence-files/IGVFFI5444WATG/), [IGVFFI1802NEVC](/sequence-files/IGVFFI1802NEVC/), [IGVFFI3327ITFG](/sequence-files/IGVFFI3327ITFG/), [IGVFFI1073RXEY](/sequence-files/IGVFFI1073RXEY/), [IGVFFI2427MOBZ](/sequence-files/IGVFFI2427MOBZ/), [IGVFFI8568QRZX](/sequence-files/IGVFFI8568QRZX/), [IGVFFI5194YEQC](/sequence-files/IGVFFI5194YEQC/), [IGVFFI7864OIDV](/sequence-files/IGVFFI7864OIDV/) 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/IGVFDS5064DHZL/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM3830RIAJ](/in-vitro-systems/IGVFSM3830RIAJ/) has in progress subobject construct library set [IGVFDS6377KNCH](/construct-library-sets/IGVFDS6377KNCH/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM3830RIAJ/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5064DHZL](/measurement-sets/IGVFDS5064DHZL/) 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/IGVFDS5064DHZL/"
}
]
},
"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/IGVFDS9477ARWI/",
"accession": "IGVFDS9477ARWI",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-Jurkat-PE2_Exp1_NegControl_AmpliconSequencing",
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-Jurkat-PE2_Exp1_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:47:21.365893+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1080XFGV/",
"accession": "IGVFDO1080XFGV",
"aliases": [
"igvf:donor_of_Jurkat"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI5444WATG/",
"accession": "IGVFFI5444WATG",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinF-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:02:01.200666+00:00",
"file_format": "fastq",
"file_size": 12606691,
"href": "/sequence-files/IGVFFI5444WATG/@@download/IGVFFI5444WATG.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/4d9132e6-53a9-415f-ad3f-d715647d3dd6/IGVFFI5444WATG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S5-BioRep2-FFRep1-BinF-PCRrep2_S76_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1802NEVC/",
"accession": "IGVFFI1802NEVC",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinF-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:42:40.528262+00:00",
"file_format": "fastq",
"file_size": 6777578,
"href": "/sequence-files/IGVFFI1802NEVC/@@download/IGVFFI1802NEVC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/184cd8be-22d8-48f1-bf43-7995ec8020b9/IGVFFI1802NEVC.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S5-BioRep2-FFRep1-BinF-PCRrep1_S20_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3327ITFG/",
"accession": "IGVFFI3327ITFG",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinF-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:08:23.858455+00:00",
"file_format": "fastq",
"file_size": 3064780,
"href": "/sequence-files/IGVFFI3327ITFG/@@download/IGVFFI3327ITFG.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/1f285848-1ab5-4825-afde-dc4ec5f5e884/IGVFFI3327ITFG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S5-BioRep2-FFRep1-BinF-PCRrep1_S20_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1073RXEY/",
"accession": "IGVFFI1073RXEY",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinF-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:14:39.383305+00:00",
"file_format": "fastq",
"file_size": 2935894,
"href": "/sequence-files/IGVFFI1073RXEY/@@download/IGVFFI1073RXEY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c6ff28c4-9659-4802-86af-0d18d54e92fc/IGVFFI1073RXEY.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S5-BioRep2-FFRep1-BinF-PCRrep2_S76_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2427MOBZ/",
"accession": "IGVFFI2427MOBZ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinF-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:27:14.647684+00:00",
"file_format": "fastq",
"file_size": 2845101,
"href": "/sequence-files/IGVFFI2427MOBZ/@@download/IGVFFI2427MOBZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/fb4bcb51-5847-4d2a-a46c-4978c522c1f4/IGVFFI2427MOBZ.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S5-BioRep2-FFRep1-BinF-PCRrep2_S76_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8568QRZX/",
"accession": "IGVFFI8568QRZX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinF-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:20:54.651633+00:00",
"file_format": "fastq",
"file_size": 2790503,
"href": "/sequence-files/IGVFFI8568QRZX/@@download/IGVFFI8568QRZX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/76badc1b-04e1-4414-9e57-eae7544cbc91/IGVFFI8568QRZX.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S5-BioRep2-FFRep1-BinF-PCRrep1_S20_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5194YEQC/",
"accession": "IGVFFI5194YEQC",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinF-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:55:23.334837+00:00",
"file_format": "fastq",
"file_size": 12424957,
"href": "/sequence-files/IGVFFI5194YEQC/@@download/IGVFFI5194YEQC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/31a4ac2c-9b2f-48ce-8bf0-382b2a8636ff/IGVFFI5194YEQC.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S5-BioRep2-FFRep1-BinF-PCRrep1_S20_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7864OIDV/",
"accession": "IGVFFI7864OIDV",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinF-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:48:58.832953+00:00",
"file_format": "fastq",
"file_size": 6902949,
"href": "/sequence-files/IGVFFI7864OIDV/@@download/IGVFFI7864OIDV.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b974267e-20f7-45e5-a9d4-97363919ac30/IGVFFI7864OIDV.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008566/",
"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S5-BioRep2-FFRep1-BinF-PCRrep2_S76_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS9162RHFP/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set. 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"
],
"release_timestamp": "2023-12-20T23:04:35.786853+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3830RIAJ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3830RIAJ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinF"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6377KNCH/",
"accession": "IGVFDS6377KNCH",
"file_set_type": "guide library",
"status": "in progress",
"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_0002796/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:Jurkat"
],
"status": "released",
"summary": "Jurkat",
"term_name": "Jurkat"
}
],
"status": "released",
"summary": "Jurkat cell line, male, Homo sapiens (sorting details: FACS bin for 90-100% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T18:42:40.528262+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": "c25e5fcb-122a-4336-8287-54249bf94cc4"
}