{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5538QQGU/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5538QQGU",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinC_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM7562TLQM](/in-vitro-systems/IGVFSM7562TLQM/) 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/IGVFSM7562TLQM/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS5538QQGU](/measurement-sets/IGVFDS5538QQGU/) has sequence file(s) [IGVFFI2164VVBX](/sequence-files/IGVFFI2164VVBX/), [IGVFFI7380ZIPT](/sequence-files/IGVFFI7380ZIPT/), [IGVFFI2500UPCT](/sequence-files/IGVFFI2500UPCT/), [IGVFFI4692LNTJ](/sequence-files/IGVFFI4692LNTJ/), [IGVFFI9528EGMD](/sequence-files/IGVFFI9528EGMD/), [IGVFFI7248ROWI](/sequence-files/IGVFFI7248ROWI/), [IGVFFI2825XLLC](/sequence-files/IGVFFI2825XLLC/), [IGVFFI4563WGEM](/sequence-files/IGVFFI4563WGEM/) 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/IGVFDS5538QQGU/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5538QQGU](/measurement-sets/IGVFDS5538QQGU/) has sequence file(s): [IGVFFI2164VVBX](/sequence-files/IGVFFI2164VVBX/), [IGVFFI7380ZIPT](/sequence-files/IGVFFI7380ZIPT/), [IGVFFI2500UPCT](/sequence-files/IGVFFI2500UPCT/), [IGVFFI4692LNTJ](/sequence-files/IGVFFI4692LNTJ/), [IGVFFI9528EGMD](/sequence-files/IGVFFI9528EGMD/), [IGVFFI7248ROWI](/sequence-files/IGVFFI7248ROWI/), [IGVFFI2825XLLC](/sequence-files/IGVFFI2825XLLC/), [IGVFFI4563WGEM](/sequence-files/IGVFFI4563WGEM/) 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/IGVFDS5538QQGU/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5538QQGU](/measurement-sets/IGVFDS5538QQGU/) 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/IGVFDS5538QQGU/"
}
]
},
"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": "2023-12-01T00:02:54.031181+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/IGVFFI2164VVBX/",
"accession": "IGVFFI2164VVBX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinC-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:05:57.732075+00:00",
"file_format": "fastq",
"file_size": 3331906,
"href": "/sequence-files/IGVFFI2164VVBX/@@download/IGVFFI2164VVBX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a4da1996-38de-4bcf-8650-bd52dd4c757e/IGVFFI2164VVBX.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_S2-BioRep1-FFRep1-BinC-PCRrep1_S3_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7380ZIPT/",
"accession": "IGVFFI7380ZIPT",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinC-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:59:21.218911+00:00",
"file_format": "fastq",
"file_size": 14561371,
"href": "/sequence-files/IGVFFI7380ZIPT/@@download/IGVFFI7380ZIPT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/12b3c48c-9cb1-4166-a12f-1f5c0b4841ad/IGVFFI7380ZIPT.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_S2-BioRep1-FFRep1-BinC-PCRrep2_S59_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2500UPCT/",
"accession": "IGVFFI2500UPCT",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinC-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:18:26.094272+00:00",
"file_format": "fastq",
"file_size": 3258036,
"href": "/sequence-files/IGVFFI2500UPCT/@@download/IGVFFI2500UPCT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/88569f1f-884b-4a72-888d-501fa2e728d3/IGVFFI2500UPCT.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_S2-BioRep1-FFRep1-BinC-PCRrep1_S3_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4692LNTJ/",
"accession": "IGVFFI4692LNTJ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinC-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:12:10.988351+00:00",
"file_format": "fastq",
"file_size": 3574462,
"href": "/sequence-files/IGVFFI4692LNTJ/@@download/IGVFFI4692LNTJ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/dcf7fd02-7eec-48d0-b221-c5b9fcf2d588/IGVFFI4692LNTJ.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_S2-BioRep1-FFRep1-BinC-PCRrep2_S59_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9528EGMD/",
"accession": "IGVFFI9528EGMD",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinC-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:52:48.593672+00:00",
"file_format": "fastq",
"file_size": 14596584,
"href": "/sequence-files/IGVFFI9528EGMD/@@download/IGVFFI9528EGMD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/007ecf1d-b2fb-4253-ab0d-5b71da8466d0/IGVFFI9528EGMD.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_S2-BioRep1-FFRep1-BinC-PCRrep1_S3_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7248ROWI/",
"accession": "IGVFFI7248ROWI",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinC-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:46:29.248746+00:00",
"file_format": "fastq",
"file_size": 7960116,
"href": "/sequence-files/IGVFFI7248ROWI/@@download/IGVFFI7248ROWI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/277e3a5c-1393-4cac-91e1-f22a5f95e128/IGVFFI7248ROWI.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_S2-BioRep1-FFRep1-BinC-PCRrep2_S59_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2825XLLC/",
"accession": "IGVFFI2825XLLC",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinC-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:40:09.658812+00:00",
"file_format": "fastq",
"file_size": 8053014,
"href": "/sequence-files/IGVFFI2825XLLC/@@download/IGVFFI2825XLLC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/de1d83b7-e5a9-4c2d-9fd4-2f1df01a9eeb/IGVFFI2825XLLC.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_S2-BioRep1-FFRep1-BinC-PCRrep1_S3_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4563WGEM/",
"accession": "IGVFFI4563WGEM",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinC-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:24:46.804414+00:00",
"file_format": "fastq",
"file_size": 3253121,
"href": "/sequence-files/IGVFFI4563WGEM/@@download/IGVFFI4563WGEM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f48bad68-921a-43f6-9efa-1fc96fb4a9a0/IGVFFI4563WGEM.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_S2-BioRep1-FFRep1-BinC-PCRrep2_S59_I2_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": "2023-12-20T23:04:42.027949+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7562TLQM/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7562TLQM",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinC"
],
"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 35-45% 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": "2023-12-05T18:40:09.658812+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": "24428ef1-1900-4b8a-ab5e-e64800d4c655"
}