{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1765SKCX/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1765SKCX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinD_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 [IGVFSM3008ENTE](/in-vitro-systems/IGVFSM3008ENTE/) 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/IGVFSM3008ENTE/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS1765SKCX](/measurement-sets/IGVFDS1765SKCX/) has sequence file(s) [IGVFFI6106FYDC](/sequence-files/IGVFFI6106FYDC/), [IGVFFI5331TZMU](/sequence-files/IGVFFI5331TZMU/), [IGVFFI7491SWVR](/sequence-files/IGVFFI7491SWVR/), [IGVFFI4799FSXO](/sequence-files/IGVFFI4799FSXO/), [IGVFFI5859NEQA](/sequence-files/IGVFFI5859NEQA/), [IGVFFI2824TFQU](/sequence-files/IGVFFI2824TFQU/), [IGVFFI3266WGZS](/sequence-files/IGVFFI3266WGZS/), [IGVFFI3886MYEM](/sequence-files/IGVFFI3886MYEM/) 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/IGVFDS1765SKCX/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1765SKCX](/measurement-sets/IGVFDS1765SKCX/) has sequence file(s): [IGVFFI6106FYDC](/sequence-files/IGVFFI6106FYDC/), [IGVFFI5331TZMU](/sequence-files/IGVFFI5331TZMU/), [IGVFFI7491SWVR](/sequence-files/IGVFFI7491SWVR/), [IGVFFI4799FSXO](/sequence-files/IGVFFI4799FSXO/), [IGVFFI5859NEQA](/sequence-files/IGVFFI5859NEQA/), [IGVFFI2824TFQU](/sequence-files/IGVFFI2824TFQU/), [IGVFFI3266WGZS](/sequence-files/IGVFFI3266WGZS/), [IGVFFI3886MYEM](/sequence-files/IGVFFI3886MYEM/) 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/IGVFDS1765SKCX/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1765SKCX](/measurement-sets/IGVFDS1765SKCX/) 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/IGVFDS1765SKCX/"
}
]
},
"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": "2023-11-30T22:47:34.187922+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/IGVFFI6106FYDC/",
"accession": "IGVFFI6106FYDC",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinD-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:50:44.412756+00:00",
"file_format": "fastq",
"file_size": 7090669,
"href": "/sequence-files/IGVFFI6106FYDC/@@download/IGVFFI6106FYDC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/cf7c036a-58b9-4b95-a07f-b4bd9e966e69/IGVFFI6106FYDC.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_S7-BioRep3-FFRep1-BinD-PCRrep2_S88_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5331TZMU/",
"accession": "IGVFFI5331TZMU",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinD-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:03:50.200976+00:00",
"file_format": "fastq",
"file_size": 12982422,
"href": "/sequence-files/IGVFFI5331TZMU/@@download/IGVFFI5331TZMU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e62a73a7-e959-4f6c-8745-3a160ce0b5ff/IGVFFI5331TZMU.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_S7-BioRep3-FFRep1-BinD-PCRrep2_S88_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7491SWVR/",
"accession": "IGVFFI7491SWVR",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinD-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:44:25.301273+00:00",
"file_format": "fastq",
"file_size": 7195744,
"href": "/sequence-files/IGVFFI7491SWVR/@@download/IGVFFI7491SWVR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/5e45abbf-01f2-4240-886c-31957ce5eca2/IGVFFI7491SWVR.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_S7-BioRep3-FFRep1-BinD-PCRrep1_S32_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4799FSXO/",
"accession": "IGVFFI4799FSXO",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinD-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:10:08.831849+00:00",
"file_format": "fastq",
"file_size": 3053278,
"href": "/sequence-files/IGVFFI4799FSXO/@@download/IGVFFI4799FSXO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/1823cf2b-971a-440f-b263-4a8d16e6a114/IGVFFI4799FSXO.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_S7-BioRep3-FFRep1-BinD-PCRrep1_S32_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5859NEQA/",
"accession": "IGVFFI5859NEQA",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinD-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T18:57:13.116066+00:00",
"file_format": "fastq",
"file_size": 13102532,
"href": "/sequence-files/IGVFFI5859NEQA/@@download/IGVFFI5859NEQA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b70447f6-8f47-4c86-8cf9-d0b2c3544327/IGVFFI5859NEQA.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_S7-BioRep3-FFRep1-BinD-PCRrep1_S32_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2824TFQU/",
"accession": "IGVFFI2824TFQU",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinD-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:28:59.619069+00:00",
"file_format": "fastq",
"file_size": 2918335,
"href": "/sequence-files/IGVFFI2824TFQU/@@download/IGVFFI2824TFQU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/1664ea04-43e4-4677-ad41-c7c31d35a66f/IGVFFI2824TFQU.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_S7-BioRep3-FFRep1-BinD-PCRrep2_S88_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3266WGZS/",
"accession": "IGVFFI3266WGZS",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinD-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:22:41.092837+00:00",
"file_format": "fastq",
"file_size": 2944153,
"href": "/sequence-files/IGVFFI3266WGZS/@@download/IGVFFI3266WGZS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/6aa2902a-accd-45b0-80b3-2cc4243a3d7d/IGVFFI3266WGZS.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_S7-BioRep3-FFRep1-BinD-PCRrep1_S32_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3886MYEM/",
"accession": "IGVFFI3886MYEM",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinD-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:16:24.301227+00:00",
"file_format": "fastq",
"file_size": 2929371,
"href": "/sequence-files/IGVFFI3886MYEM/@@download/IGVFFI3886MYEM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/4b0e8fd8-2df1-40a9-8700-a797d2491c64/IGVFFI3886MYEM.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_S7-BioRep3-FFRep1-BinD-PCRrep2_S88_I1_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": "2023-12-20T23:05:05.484878+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3008ENTE/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3008ENTE",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinD"
],
"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 55-65% 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": "2023-12-05T18:44:25.301273+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": "aa41b74c-1e0e-47f2-b20e-51bc95acb50a"
}