{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3533ZJCT/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3533ZJCT",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-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": "missing sequencing kit",
"detail": "Measurement set [IGVFDS3533ZJCT](/measurement-sets/IGVFDS3533ZJCT/) has sequence file(s) [IGVFFI4445TFYF](/sequence-files/IGVFFI4445TFYF/), [IGVFFI4306THVP](/sequence-files/IGVFFI4306THVP/), [IGVFFI2646PTDS](/sequence-files/IGVFFI2646PTDS/), [IGVFFI0835WSQW](/sequence-files/IGVFFI0835WSQW/), [IGVFFI7308ELUD](/sequence-files/IGVFFI7308ELUD/), [IGVFFI8659LEJT](/sequence-files/IGVFFI8659LEJT/), [IGVFFI5228JOAZ](/sequence-files/IGVFFI5228JOAZ/), [IGVFFI5270ZLOL](/sequence-files/IGVFFI5270ZLOL/) 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/IGVFDS3533ZJCT/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3533ZJCT](/measurement-sets/IGVFDS3533ZJCT/) has sequence file(s): [IGVFFI4445TFYF](/sequence-files/IGVFFI4445TFYF/), [IGVFFI4306THVP](/sequence-files/IGVFFI4306THVP/), [IGVFFI2646PTDS](/sequence-files/IGVFFI2646PTDS/), [IGVFFI0835WSQW](/sequence-files/IGVFFI0835WSQW/), [IGVFFI7308ELUD](/sequence-files/IGVFFI7308ELUD/), [IGVFFI8659LEJT](/sequence-files/IGVFFI8659LEJT/), [IGVFFI5228JOAZ](/sequence-files/IGVFFI5228JOAZ/), [IGVFFI5270ZLOL](/sequence-files/IGVFFI5270ZLOL/) 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/IGVFDS3533ZJCT/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM6792CERQ](/in-vitro-systems/IGVFSM6792CERQ/) 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/IGVFSM6792CERQ/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS3533ZJCT](/measurement-sets/IGVFDS3533ZJCT/) 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/IGVFDS3533ZJCT/"
}
]
},
"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": "2023-11-30T22:47:59.077021+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/IGVFFI4445TFYF/",
"accession": "IGVFFI4445TFYF",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinE-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:22:23.508927+00:00",
"file_format": "fastq",
"file_size": 3259646,
"href": "/sequence-files/IGVFFI4445TFYF/@@download/IGVFFI4445TFYF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/6e3125f0-faa8-42b5-a35a-47ce77dcfca8/IGVFFI4445TFYF.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_pPPIF2_S13-BioRep1-FFRep2-BinE-PCRrep2_S181_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4306THVP/",
"accession": "IGVFFI4306THVP",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinE-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:13:55.945152+00:00",
"file_format": "fastq",
"file_size": 13684327,
"href": "/sequence-files/IGVFFI4306THVP/@@download/IGVFFI4306THVP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/ca5ee44d-c34e-44dc-846c-cb429cf8586e/IGVFFI4306THVP.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_pPPIF2_S13-BioRep1-FFRep2-BinE-PCRrep2_S181_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2646PTDS/",
"accession": "IGVFFI2646PTDS",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinE-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:30:44.125916+00:00",
"file_format": "fastq",
"file_size": 3067628,
"href": "/sequence-files/IGVFFI2646PTDS/@@download/IGVFFI2646PTDS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f21a4a65-fdea-464d-bbeb-4d97a99af3d8/IGVFFI2646PTDS.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_pPPIF2_S13-BioRep1-FFRep2-BinE-PCRrep2_S181_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0835WSQW/",
"accession": "IGVFFI0835WSQW",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinE-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:40:45.086838+00:00",
"file_format": "fastq",
"file_size": 14188946,
"href": "/sequence-files/IGVFFI0835WSQW/@@download/IGVFFI0835WSQW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/dac5a91b-b202-42a1-aae1-8400f7809c96/IGVFFI0835WSQW.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_pPPIF2_S13-BioRep1-FFRep2-BinE-PCRrep1_S124_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7308ELUD/",
"accession": "IGVFFI7308ELUD",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinE-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:49:18.370041+00:00",
"file_format": "fastq",
"file_size": 3235230,
"href": "/sequence-files/IGVFFI7308ELUD/@@download/IGVFFI7308ELUD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/66886c91-de21-4707-a967-3700e35a6b3f/IGVFFI7308ELUD.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_pPPIF2_S13-BioRep1-FFRep2-BinE-PCRrep1_S124_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8659LEJT/",
"accession": "IGVFFI8659LEJT",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinE-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:57:26.418349+00:00",
"file_format": "fastq",
"file_size": 3162934,
"href": "/sequence-files/IGVFFI8659LEJT/@@download/IGVFFI8659LEJT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/8e285aec-fcd5-4534-a5bf-237d2eabbdc4/IGVFFI8659LEJT.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_pPPIF2_S13-BioRep1-FFRep2-BinE-PCRrep1_S124_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5228JOAZ/",
"accession": "IGVFFI5228JOAZ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinE-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:32:21.618152+00:00",
"file_format": "fastq",
"file_size": 7553034,
"href": "/sequence-files/IGVFFI5228JOAZ/@@download/IGVFFI5228JOAZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/30483979-bae4-4fbe-9456-84a46dce9296/IGVFFI5228JOAZ.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_pPPIF2_S13-BioRep1-FFRep2-BinE-PCRrep1_S124_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5270ZLOL/",
"accession": "IGVFFI5270ZLOL",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep2-BinE-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:05:37.819954+00:00",
"file_format": "fastq",
"file_size": 7313781,
"href": "/sequence-files/IGVFFI5270ZLOL/@@download/IGVFFI5270ZLOL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/c058d117-d2ec-407f-83a1-be45e2a3946d/IGVFFI5270ZLOL.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_pPPIF2_S13-BioRep1-FFRep2-BinE-PCRrep2_S181_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1863TJOE/"
],
"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": "2023-12-20T23:03:40.405253+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6792CERQ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6792CERQ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-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) treated with 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours, modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/df02c0d4-f796-4f77-bfbc-388cdbfcc615/",
"status": "released",
"treatment_term_name": "T-cell surface glycoprotein CD3 gamma chain"
},
{
"@id": "/treatments/42b3c61d-38de-4bd2-bb39-33c125a417cb/",
"status": "released",
"treatment_term_name": "phorbol 13-acetate 12-myristate"
}
]
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T19:32:21.618152+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": "9b7d7cb6-1aa6-40fd-af88-312a3b36a8c1"
}