{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8094KCRL/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8094KCRL",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinB_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 [IGVFDS8094KCRL](/measurement-sets/IGVFDS8094KCRL/) has sequence file(s) [IGVFFI2728OZPD](/sequence-files/IGVFFI2728OZPD/), [IGVFFI6350DPUO](/sequence-files/IGVFFI6350DPUO/), [IGVFFI6108YFUX](/sequence-files/IGVFFI6108YFUX/), [IGVFFI9667XFSJ](/sequence-files/IGVFFI9667XFSJ/), [IGVFFI1407IPQA](/sequence-files/IGVFFI1407IPQA/), [IGVFFI3878YIZT](/sequence-files/IGVFFI3878YIZT/), [IGVFFI2190DJJL](/sequence-files/IGVFFI2190DJJL/), [IGVFFI0950AIOF](/sequence-files/IGVFFI0950AIOF/) 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/IGVFDS8094KCRL/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8094KCRL](/measurement-sets/IGVFDS8094KCRL/) has sequence file(s): [IGVFFI2728OZPD](/sequence-files/IGVFFI2728OZPD/), [IGVFFI6350DPUO](/sequence-files/IGVFFI6350DPUO/), [IGVFFI6108YFUX](/sequence-files/IGVFFI6108YFUX/), [IGVFFI9667XFSJ](/sequence-files/IGVFFI9667XFSJ/), [IGVFFI1407IPQA](/sequence-files/IGVFFI1407IPQA/), [IGVFFI3878YIZT](/sequence-files/IGVFFI3878YIZT/), [IGVFFI2190DJJL](/sequence-files/IGVFFI2190DJJL/), [IGVFFI0950AIOF](/sequence-files/IGVFFI0950AIOF/) 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/IGVFDS8094KCRL/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM3608ERFP](/in-vitro-systems/IGVFSM3608ERFP/) 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/IGVFSM3608ERFP/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS8094KCRL](/measurement-sets/IGVFDS8094KCRL/) 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/IGVFDS8094KCRL/"
}
]
},
"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": "2023-11-30T22:47:16.848872+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/IGVFFI2728OZPD/",
"accession": "IGVFFI2728OZPD",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinB-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:07:49.041106+00:00",
"file_format": "fastq",
"file_size": 3279215,
"href": "/sequence-files/IGVFFI2728OZPD/@@download/IGVFFI2728OZPD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/31bca9b9-67dc-4c13-8185-75de9196320d/IGVFFI2728OZPD.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-BinB-PCRrep1_S16_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6350DPUO/",
"accession": "IGVFFI6350DPUO",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinB-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:48:23.781323+00:00",
"file_format": "fastq",
"file_size": 7795445,
"href": "/sequence-files/IGVFFI6350DPUO/@@download/IGVFFI6350DPUO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f9b18862-8939-4cb7-9e7b-e5712d32ebaa/IGVFFI6350DPUO.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-BinB-PCRrep2_S72_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6108YFUX/",
"accession": "IGVFFI6108YFUX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinB-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:54:47.193057+00:00",
"file_format": "fastq",
"file_size": 14030442,
"href": "/sequence-files/IGVFFI6108YFUX/@@download/IGVFFI6108YFUX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/d126dd09-1f13-4d0a-b329-6009a0fe8e2c/IGVFFI6108YFUX.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-BinB-PCRrep1_S16_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9667XFSJ/",
"accession": "IGVFFI9667XFSJ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinB-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:26:40.540793+00:00",
"file_format": "fastq",
"file_size": 3177576,
"href": "/sequence-files/IGVFFI9667XFSJ/@@download/IGVFFI9667XFSJ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a9c008e0-7fdd-42d1-a0b8-34a064d72c09/IGVFFI9667XFSJ.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-BinB-PCRrep2_S72_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1407IPQA/",
"accession": "IGVFFI1407IPQA",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinB-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:14:04.470931+00:00",
"file_format": "fastq",
"file_size": 3219166,
"href": "/sequence-files/IGVFFI1407IPQA/@@download/IGVFFI1407IPQA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/0cb1fe3a-a3c8-44f6-bc62-ca0670aa091f/IGVFFI1407IPQA.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-BinB-PCRrep2_S72_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3878YIZT/",
"accession": "IGVFFI3878YIZT",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinB-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:01:24.721854+00:00",
"file_format": "fastq",
"file_size": 14168583,
"href": "/sequence-files/IGVFFI3878YIZT/@@download/IGVFFI3878YIZT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/1da6ec53-f20a-4bc4-bbdc-329fe1be5d47/IGVFFI3878YIZT.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-BinB-PCRrep2_S72_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2190DJJL/",
"accession": "IGVFFI2190DJJL",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinB-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:20:19.804318+00:00",
"file_format": "fastq",
"file_size": 3147071,
"href": "/sequence-files/IGVFFI2190DJJL/@@download/IGVFFI2190DJJL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a6e44a6b-4f40-49cd-b9b2-fccfe0101b84/IGVFFI2190DJJL.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-BinB-PCRrep1_S16_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0950AIOF/",
"accession": "IGVFFI0950AIOF",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinB-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:42:05.440309+00:00",
"file_format": "fastq",
"file_size": 7670603,
"href": "/sequence-files/IGVFFI0950AIOF/@@download/IGVFFI0950AIOF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/9b56f515-5b7c-420c-8ca8-fdd6a0d9baf5/IGVFFI0950AIOF.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-BinB-PCRrep1_S16_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": "2023-12-20T23:09:53.150017+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3608ERFP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3608ERFP",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep1-BinB"
],
"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 11-20% 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": "2023-12-05T18:42:05.440309+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": "37aaefba-df3a-4d18-9ba5-bb257557ad6c"
}