{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6080NOYA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6080NOYA",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinC_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 [IGVFDS6080NOYA](/measurement-sets/IGVFDS6080NOYA/) has sequence file(s) [IGVFFI6543NKQM](/sequence-files/IGVFFI6543NKQM/), [IGVFFI2371SEQS](/sequence-files/IGVFFI2371SEQS/), [IGVFFI3348OHQW](/sequence-files/IGVFFI3348OHQW/), [IGVFFI8445BPWI](/sequence-files/IGVFFI8445BPWI/), [IGVFFI1903VUBK](/sequence-files/IGVFFI1903VUBK/), [IGVFFI6002XWSL](/sequence-files/IGVFFI6002XWSL/), [IGVFFI5464GKYM](/sequence-files/IGVFFI5464GKYM/), [IGVFFI7554KOVE](/sequence-files/IGVFFI7554KOVE/) 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/IGVFDS6080NOYA/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS6080NOYA](/measurement-sets/IGVFDS6080NOYA/) has sequence file(s): [IGVFFI6543NKQM](/sequence-files/IGVFFI6543NKQM/), [IGVFFI2371SEQS](/sequence-files/IGVFFI2371SEQS/), [IGVFFI3348OHQW](/sequence-files/IGVFFI3348OHQW/), [IGVFFI8445BPWI](/sequence-files/IGVFFI8445BPWI/), [IGVFFI1903VUBK](/sequence-files/IGVFFI1903VUBK/), [IGVFFI6002XWSL](/sequence-files/IGVFFI6002XWSL/), [IGVFFI5464GKYM](/sequence-files/IGVFFI5464GKYM/), [IGVFFI7554KOVE](/sequence-files/IGVFFI7554KOVE/) 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/IGVFDS6080NOYA/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM2293MFSW](/in-vitro-systems/IGVFSM2293MFSW/) 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/IGVFSM2293MFSW/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6080NOYA](/measurement-sets/IGVFDS6080NOYA/) 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/IGVFDS6080NOYA/"
}
]
},
"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": "2023-11-30T22:47:41.343162+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/IGVFFI6543NKQM/",
"accession": "IGVFFI6543NKQM",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinC-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:23:36.942022+00:00",
"file_format": "fastq",
"file_size": 3126275,
"href": "/sequence-files/IGVFFI6543NKQM/@@download/IGVFFI6543NKQM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/ddedadd5-5428-447e-aae2-e9fd18866c06/IGVFFI6543NKQM.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_S8-BioRep3-FFRep2-BinC-PCRrep1_S38_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2371SEQS/",
"accession": "IGVFFI2371SEQS",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinC-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:17:16.588906+00:00",
"file_format": "fastq",
"file_size": 3448895,
"href": "/sequence-files/IGVFFI2371SEQS/@@download/IGVFFI2371SEQS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/7cc9850b-0b25-4a33-b05d-2ff244c7fadf/IGVFFI2371SEQS.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_S8-BioRep3-FFRep2-BinC-PCRrep2_S94_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3348OHQW/",
"accession": "IGVFFI3348OHQW",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinC-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:04:45.354353+00:00",
"file_format": "fastq",
"file_size": 14560772,
"href": "/sequence-files/IGVFFI3348OHQW/@@download/IGVFFI3348OHQW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/659cb6f6-2372-4c6c-b15c-53fcbe352ad1/IGVFFI3348OHQW.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_S8-BioRep3-FFRep2-BinC-PCRrep2_S94_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8445BPWI/",
"accession": "IGVFFI8445BPWI",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinC-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:11:00.889645+00:00",
"file_format": "fastq",
"file_size": 3253602,
"href": "/sequence-files/IGVFFI8445BPWI/@@download/IGVFFI8445BPWI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c0d18950-eaca-406d-b492-1049767df648/IGVFFI8445BPWI.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_S8-BioRep3-FFRep2-BinC-PCRrep1_S38_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1903VUBK/",
"accession": "IGVFFI1903VUBK",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinC-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:45:19.248199+00:00",
"file_format": "fastq",
"file_size": 7649234,
"href": "/sequence-files/IGVFFI1903VUBK/@@download/IGVFFI1903VUBK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2eb66fac-346d-40bb-a08c-36cd8ff15139/IGVFFI1903VUBK.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_S8-BioRep3-FFRep2-BinC-PCRrep1_S38_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6002XWSL/",
"accession": "IGVFFI6002XWSL",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinC-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:58:07.875056+00:00",
"file_format": "fastq",
"file_size": 13901200,
"href": "/sequence-files/IGVFFI6002XWSL/@@download/IGVFFI6002XWSL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/70024b1e-281f-4b5b-b13f-037ea5f5103d/IGVFFI6002XWSL.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_S8-BioRep3-FFRep2-BinC-PCRrep1_S38_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5464GKYM/",
"accession": "IGVFFI5464GKYM",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinC-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:29:51.762159+00:00",
"file_format": "fastq",
"file_size": 3289662,
"href": "/sequence-files/IGVFFI5464GKYM/@@download/IGVFFI5464GKYM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b5655d5c-95fc-41ed-ad3d-171dd5317ecb/IGVFFI5464GKYM.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_S8-BioRep3-FFRep2-BinC-PCRrep2_S94_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7554KOVE/",
"accession": "IGVFFI7554KOVE",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinC-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:51:37.049088+00:00",
"file_format": "fastq",
"file_size": 7912087,
"href": "/sequence-files/IGVFFI7554KOVE/@@download/IGVFFI7554KOVE.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/78aaf174-678f-409b-aef9-dfa0b5fd5b26/IGVFFI7554KOVE.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_S8-BioRep3-FFRep2-BinC-PCRrep2_S94_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": "2023-12-20T23:11:03.478094+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2293MFSW/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2293MFSW",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep2-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": "2023-12-05T18:45:19.248199+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": "9ec6cd85-6157-4a2a-b41c-024f89c9a62e"
}