{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1466VGTF/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1466VGTF",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-BinA_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 [IGVFSM2681JPHQ](/in-vitro-systems/IGVFSM2681JPHQ/) 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/IGVFSM2681JPHQ/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS1466VGTF](/measurement-sets/IGVFDS1466VGTF/) has sequence file(s) [IGVFFI8093WBFH](/sequence-files/IGVFFI8093WBFH/), [IGVFFI4004QGCL](/sequence-files/IGVFFI4004QGCL/), [IGVFFI0960PANZ](/sequence-files/IGVFFI0960PANZ/), [IGVFFI1051OAYW](/sequence-files/IGVFFI1051OAYW/), [IGVFFI2946JGVC](/sequence-files/IGVFFI2946JGVC/), [IGVFFI7327BMUR](/sequence-files/IGVFFI7327BMUR/), [IGVFFI1618TZCZ](/sequence-files/IGVFFI1618TZCZ/), [IGVFFI6810ECVC](/sequence-files/IGVFFI6810ECVC/) 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/IGVFDS1466VGTF/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1466VGTF](/measurement-sets/IGVFDS1466VGTF/) has sequence file(s): [IGVFFI8093WBFH](/sequence-files/IGVFFI8093WBFH/), [IGVFFI4004QGCL](/sequence-files/IGVFFI4004QGCL/), [IGVFFI0960PANZ](/sequence-files/IGVFFI0960PANZ/), [IGVFFI1051OAYW](/sequence-files/IGVFFI1051OAYW/), [IGVFFI2946JGVC](/sequence-files/IGVFFI2946JGVC/), [IGVFFI7327BMUR](/sequence-files/IGVFFI7327BMUR/), [IGVFFI1618TZCZ](/sequence-files/IGVFFI1618TZCZ/), [IGVFFI6810ECVC](/sequence-files/IGVFFI6810ECVC/) 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/IGVFDS1466VGTF/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1466VGTF](/measurement-sets/IGVFDS1466VGTF/) 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/IGVFDS1466VGTF/"
}
]
},
"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": "2023-11-30T22:48:32.725565+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/IGVFFI8093WBFH/",
"accession": "IGVFFI8093WBFH",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-BinA-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:10:11.111580+00:00",
"file_format": "fastq",
"file_size": 8183702,
"href": "/sequence-files/IGVFFI8093WBFH/@@download/IGVFFI8093WBFH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f9ead59f-16a1-4a99-9971-256ebd4b74f3/IGVFFI8093WBFH.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_S19-BioRep4-FFRep1-BinA-PCRrep2_S212_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4004QGCL/",
"accession": "IGVFFI4004QGCL",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-BinA-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:18:40.097555+00:00",
"file_format": "fastq",
"file_size": 15043829,
"href": "/sequence-files/IGVFFI4004QGCL/@@download/IGVFFI4004QGCL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/40acbca5-7c65-405b-a7f2-89e9a092c5d3/IGVFFI4004QGCL.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_S19-BioRep4-FFRep1-BinA-PCRrep2_S212_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0960PANZ/",
"accession": "IGVFFI0960PANZ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-BinA-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:01:56.323587+00:00",
"file_format": "fastq",
"file_size": 2927122,
"href": "/sequence-files/IGVFFI0960PANZ/@@download/IGVFFI0960PANZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/8dcb0e7e-14fe-4b53-984e-91742c19d84a/IGVFFI0960PANZ.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_S19-BioRep4-FFRep1-BinA-PCRrep1_S155_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1051OAYW/",
"accession": "IGVFFI1051OAYW",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-BinA-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:53:48.818935+00:00",
"file_format": "fastq",
"file_size": 3014307,
"href": "/sequence-files/IGVFFI1051OAYW/@@download/IGVFFI1051OAYW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/3e217bc3-bd14-4d42-9f28-6226ab0eae86/IGVFFI1051OAYW.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_S19-BioRep4-FFRep1-BinA-PCRrep1_S155_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2946JGVC/",
"accession": "IGVFFI2946JGVC",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-BinA-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:27:02.202061+00:00",
"file_format": "fastq",
"file_size": 3361305,
"href": "/sequence-files/IGVFFI2946JGVC/@@download/IGVFFI2946JGVC.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/814d43e9-300f-4404-b963-06daaf7030b4/IGVFFI2946JGVC.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S19-BioRep4-FFRep1-BinA-PCRrep2_S212_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7327BMUR/",
"accession": "IGVFFI7327BMUR",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-BinA-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:35:15.337795+00:00",
"file_format": "fastq",
"file_size": 3392249,
"href": "/sequence-files/IGVFFI7327BMUR/@@download/IGVFFI7327BMUR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/2f1543c8-1956-47ab-a05a-cf2894cd7ff1/IGVFFI7327BMUR.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_S19-BioRep4-FFRep1-BinA-PCRrep2_S212_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1618TZCZ/",
"accession": "IGVFFI1618TZCZ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-BinA-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:45:29.171696+00:00",
"file_format": "fastq",
"file_size": 12815387,
"href": "/sequence-files/IGVFFI1618TZCZ/@@download/IGVFFI1618TZCZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/86e41c0a-8e82-4545-bcba-bb57957b85e2/IGVFFI1618TZCZ.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S19-BioRep4-FFRep1-BinA-PCRrep1_S155_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6810ECVC/",
"accession": "IGVFFI6810ECVC",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-BinA-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:36:59.775637+00:00",
"file_format": "fastq",
"file_size": 7004925,
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S19-BioRep4-FFRep1-BinA-PCRrep1_S155_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": "2023-12-20T23:04:52.539710+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM2681JPHQ/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2681JPHQ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-BinA"
],
"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 0-10% 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": "2023-12-05T19:36:59.775637+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": "ba407470-2c45-4ef2-b4ed-84c3babc84b8"
}