{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3316IDPS/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3316IDPS",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-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 [IGVFSM9490SYQE](/in-vitro-systems/IGVFSM9490SYQE/) 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/IGVFSM9490SYQE/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS3316IDPS](/measurement-sets/IGVFDS3316IDPS/) has sequence file(s) [IGVFFI5481BJMH](/sequence-files/IGVFFI5481BJMH/), [IGVFFI8055HUBU](/sequence-files/IGVFFI8055HUBU/), [IGVFFI4133DVTI](/sequence-files/IGVFFI4133DVTI/), [IGVFFI7024WSRG](/sequence-files/IGVFFI7024WSRG/), [IGVFFI4714BSOW](/sequence-files/IGVFFI4714BSOW/), [IGVFFI0161NFSI](/sequence-files/IGVFFI0161NFSI/), [IGVFFI2719DACK](/sequence-files/IGVFFI2719DACK/), [IGVFFI4271DVOC](/sequence-files/IGVFFI4271DVOC/) 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/IGVFDS3316IDPS/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3316IDPS](/measurement-sets/IGVFDS3316IDPS/) has sequence file(s): [IGVFFI5481BJMH](/sequence-files/IGVFFI5481BJMH/), [IGVFFI8055HUBU](/sequence-files/IGVFFI8055HUBU/), [IGVFFI4133DVTI](/sequence-files/IGVFFI4133DVTI/), [IGVFFI7024WSRG](/sequence-files/IGVFFI7024WSRG/), [IGVFFI4714BSOW](/sequence-files/IGVFFI4714BSOW/), [IGVFFI0161NFSI](/sequence-files/IGVFFI0161NFSI/), [IGVFFI2719DACK](/sequence-files/IGVFFI2719DACK/), [IGVFFI4271DVOC](/sequence-files/IGVFFI4271DVOC/) 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/IGVFDS3316IDPS/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS3316IDPS](/measurement-sets/IGVFDS3316IDPS/) 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/IGVFDS3316IDPS/"
}
]
},
"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": "2023-11-30T22:47:50.231170+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/IGVFFI5481BJMH/",
"accession": "IGVFFI5481BJMH",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinE-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:12:52.036103+00:00",
"file_format": "fastq",
"file_size": 13851505,
"href": "/sequence-files/IGVFFI5481BJMH/@@download/IGVFFI5481BJMH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/89431d6c-c4c7-46d8-bbf7-a937107603eb/IGVFFI5481BJMH.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_S12-BioRep1-FFRep1-BinE-PCRrep2_S174_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8055HUBU/",
"accession": "IGVFFI8055HUBU",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinE-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:48:13.348226+00:00",
"file_format": "fastq",
"file_size": 3264402,
"href": "/sequence-files/IGVFFI8055HUBU/@@download/IGVFFI8055HUBU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/25b32365-3e79-4a55-963f-4e4cf9e178c1/IGVFFI8055HUBU.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_S12-BioRep1-FFRep1-BinE-PCRrep1_S117_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4133DVTI/",
"accession": "IGVFFI4133DVTI",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinE-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:56:25.574482+00:00",
"file_format": "fastq",
"file_size": 3208498,
"href": "/sequence-files/IGVFFI4133DVTI/@@download/IGVFFI4133DVTI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/4130c839-8be3-4bd6-a696-e698985d04cf/IGVFFI4133DVTI.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_S12-BioRep1-FFRep1-BinE-PCRrep1_S117_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7024WSRG/",
"accession": "IGVFFI7024WSRG",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinE-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:21:22.760244+00:00",
"file_format": "fastq",
"file_size": 3175816,
"href": "/sequence-files/IGVFFI7024WSRG/@@download/IGVFFI7024WSRG.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/18707c28-3d98-46c9-96fe-b917eb388515/IGVFFI7024WSRG.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_S12-BioRep1-FFRep1-BinE-PCRrep2_S174_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4714BSOW/",
"accession": "IGVFFI4714BSOW",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinE-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:31:19.841725+00:00",
"file_format": "fastq",
"file_size": 7664601,
"href": "/sequence-files/IGVFFI4714BSOW/@@download/IGVFFI4714BSOW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/03b49666-6b63-4246-819b-471d02ac2336/IGVFFI4714BSOW.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_S12-BioRep1-FFRep1-BinE-PCRrep1_S117_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0161NFSI/",
"accession": "IGVFFI0161NFSI",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinE-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:29:39.391026+00:00",
"file_format": "fastq",
"file_size": 3112104,
"href": "/sequence-files/IGVFFI0161NFSI/@@download/IGVFFI0161NFSI.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/9486c28a-8763-429c-8ec4-f6eeca36b2ef/IGVFFI0161NFSI.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_S12-BioRep1-FFRep1-BinE-PCRrep2_S174_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2719DACK/",
"accession": "IGVFFI2719DACK",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinE-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:04:33.374870+00:00",
"file_format": "fastq",
"file_size": 7442716,
"href": "/sequence-files/IGVFFI2719DACK/@@download/IGVFFI2719DACK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/0affcda1-21a4-4770-960e-4b1657219599/IGVFFI2719DACK.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_S12-BioRep1-FFRep1-BinE-PCRrep2_S174_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4271DVOC/",
"accession": "IGVFFI4271DVOC",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinE-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:39:40.694410+00:00",
"file_format": "fastq",
"file_size": 14353957,
"href": "/sequence-files/IGVFFI4271DVOC/@@download/IGVFFI4271DVOC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/cc34abda-eaf6-4fd2-a9f8-73ad9b157af9/IGVFFI4271DVOC.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_S12-BioRep1-FFRep1-BinE-PCRrep1_S117_R2_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": "2023-12-20T23:04:26.937755+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9490SYQE/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9490SYQE",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-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": "2023-12-05T19:31:19.841725+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": "1f45f931-4c33-4c3d-98c0-7dd32c9eb32f"
}