{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2464NZAA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2464NZAA",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinE_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 [IGVFSM8611NTVR](/in-vitro-systems/IGVFSM8611NTVR/) 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/IGVFSM8611NTVR/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2464NZAA](/measurement-sets/IGVFDS2464NZAA/) has sequence file(s) [IGVFFI5964MBKT](/sequence-files/IGVFFI5964MBKT/), [IGVFFI0432IZIX](/sequence-files/IGVFFI0432IZIX/), [IGVFFI6133CQRE](/sequence-files/IGVFFI6133CQRE/), [IGVFFI2830LRGH](/sequence-files/IGVFFI2830LRGH/), [IGVFFI2365BQWL](/sequence-files/IGVFFI2365BQWL/), [IGVFFI6504WAKT](/sequence-files/IGVFFI6504WAKT/), [IGVFFI9806ADFX](/sequence-files/IGVFFI9806ADFX/), [IGVFFI7021YYQY](/sequence-files/IGVFFI7021YYQY/) 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/IGVFDS2464NZAA/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2464NZAA](/measurement-sets/IGVFDS2464NZAA/) has sequence file(s): [IGVFFI5964MBKT](/sequence-files/IGVFFI5964MBKT/), [IGVFFI0432IZIX](/sequence-files/IGVFFI0432IZIX/), [IGVFFI6133CQRE](/sequence-files/IGVFFI6133CQRE/), [IGVFFI2830LRGH](/sequence-files/IGVFFI2830LRGH/), [IGVFFI2365BQWL](/sequence-files/IGVFFI2365BQWL/), [IGVFFI6504WAKT](/sequence-files/IGVFFI6504WAKT/), [IGVFFI9806ADFX](/sequence-files/IGVFFI9806ADFX/), [IGVFFI7021YYQY](/sequence-files/IGVFFI7021YYQY/) 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/IGVFDS2464NZAA/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2464NZAA](/measurement-sets/IGVFDS2464NZAA/) 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/IGVFDS2464NZAA/"
}
]
},
"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": "2023-11-30T22:47:28.187760+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/IGVFFI5964MBKT/",
"accession": "IGVFFI5964MBKT",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinE-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:49:51.673107+00:00",
"file_format": "fastq",
"file_size": 7791336,
"href": "/sequence-files/IGVFFI5964MBKT/@@download/IGVFFI5964MBKT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/755020d6-a44a-4717-91ae-196931265f75/IGVFFI5964MBKT.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_S6-BioRep2-FFRep2-BinE-PCRrep2_S82_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0432IZIX/",
"accession": "IGVFFI0432IZIX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinE-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:21:48.464663+00:00",
"file_format": "fastq",
"file_size": 3201116,
"href": "/sequence-files/IGVFFI0432IZIX/@@download/IGVFFI0432IZIX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/21aa2a21-063e-49d5-a512-bcfb588458a2/IGVFFI0432IZIX.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_S6-BioRep2-FFRep2-BinE-PCRrep1_S26_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6133CQRE/",
"accession": "IGVFFI6133CQRE",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinE-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:02:55.597780+00:00",
"file_format": "fastq",
"file_size": 14346948,
"href": "/sequence-files/IGVFFI6133CQRE/@@download/IGVFFI6133CQRE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f779b262-b0ea-46d3-a188-df6db3d3dd0a/IGVFFI6133CQRE.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_S6-BioRep2-FFRep2-BinE-PCRrep2_S82_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2830LRGH/",
"accession": "IGVFFI2830LRGH",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinE-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:15:31.918595+00:00",
"file_format": "fastq",
"file_size": 3282027,
"href": "/sequence-files/IGVFFI2830LRGH/@@download/IGVFFI2830LRGH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f7b50ea1-147c-48aa-a9cd-b1b803bc5cbe/IGVFFI2830LRGH.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_S6-BioRep2-FFRep2-BinE-PCRrep2_S82_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2365BQWL/",
"accession": "IGVFFI2365BQWL",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinE-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:09:16.539560+00:00",
"file_format": "fastq",
"file_size": 3259938,
"href": "/sequence-files/IGVFFI2365BQWL/@@download/IGVFFI2365BQWL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/5b66b726-7ee6-4400-b7e6-06e6b9c7afa6/IGVFFI2365BQWL.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_S6-BioRep2-FFRep2-BinE-PCRrep1_S26_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6504WAKT/",
"accession": "IGVFFI6504WAKT",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinE-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:28:07.458964+00:00",
"file_format": "fastq",
"file_size": 3220361,
"href": "/sequence-files/IGVFFI6504WAKT/@@download/IGVFFI6504WAKT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c6fbae76-bf62-41cb-b303-912c2bb29a77/IGVFFI6504WAKT.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_S6-BioRep2-FFRep2-BinE-PCRrep2_S82_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9806ADFX/",
"accession": "IGVFFI9806ADFX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinE-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:56:18.191107+00:00",
"file_format": "fastq",
"file_size": 14279453,
"href": "/sequence-files/IGVFFI9806ADFX/@@download/IGVFFI9806ADFX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c084e7a7-22e6-41aa-a9ae-9c03d8086821/IGVFFI9806ADFX.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_S6-BioRep2-FFRep2-BinE-PCRrep1_S26_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7021YYQY/",
"accession": "IGVFFI7021YYQY",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinE-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:43:32.903073+00:00",
"file_format": "fastq",
"file_size": 7814708,
"href": "/sequence-files/IGVFFI7021YYQY/@@download/IGVFFI7021YYQY.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/cdca0f62-2845-4b81-add8-72a4136fcc1a/IGVFFI7021YYQY.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_S6-BioRep2-FFRep2-BinE-PCRrep1_S26_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": "2023-12-20T23:05:01.513339+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8611NTVR/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8611NTVR",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep2-FFrep2-BinE"
],
"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 80-90% 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": "2023-12-05T18:43:32.903073+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": "4d88c230-9a43-4859-a110-5bfdfe7ca41d"
}