{
"@context": "/terms/",
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"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2950WXZR",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinD_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"assay_slims": [
"CRISPR screens"
],
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS2950WXZR](/measurement-sets/IGVFDS2950WXZR/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_file_set_missing_publication",
"path": "/measurement-sets/IGVFDS2950WXZR/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS2950WXZR](/measurement-sets/IGVFDS2950WXZR/) has sequence file(s) [IGVFFI1827IVYF](/sequence-files/IGVFFI1827IVYF/), [IGVFFI3995GHXU](/sequence-files/IGVFFI3995GHXU/), [IGVFFI7134JKWO](/sequence-files/IGVFFI7134JKWO/), [IGVFFI9482QSDK](/sequence-files/IGVFFI9482QSDK/), [IGVFFI5885CAZU](/sequence-files/IGVFFI5885CAZU/), [IGVFFI1585CPUX](/sequence-files/IGVFFI1585CPUX/), [IGVFFI0675ERAV](/sequence-files/IGVFFI0675ERAV/), [IGVFFI0786VNUG](/sequence-files/IGVFFI0786VNUG/) which lack specification of a `sequencing_kit`. Sequence files in a file set associated wtih bulk data should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS2950WXZR/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2950WXZR](/measurement-sets/IGVFDS2950WXZR/) has sequence file(s): [IGVFFI1827IVYF](/sequence-files/IGVFFI1827IVYF/), [IGVFFI3995GHXU](/sequence-files/IGVFFI3995GHXU/), [IGVFFI7134JKWO](/sequence-files/IGVFFI7134JKWO/), [IGVFFI9482QSDK](/sequence-files/IGVFFI9482QSDK/), [IGVFFI5885CAZU](/sequence-files/IGVFFI5885CAZU/), [IGVFFI1585CPUX](/sequence-files/IGVFFI1585CPUX/), [IGVFFI0675ERAV](/sequence-files/IGVFFI0675ERAV/), [IGVFFI0786VNUG](/sequence-files/IGVFFI0786VNUG/) which do not have any `seqspecs`. Sequence files in a file set associated with bulk data are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS2950WXZR/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM1865XXUT](/in-vitro-systems/IGVFSM1865XXUT/) 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/IGVFSM1865XXUT/"
},
{
"category": "missing publication",
"detail": "In vitro system [IGVFSM1865XXUT](/in-vitro-systems/IGVFSM1865XXUT/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_sample_missing_publication",
"path": "/in-vitro-systems/IGVFSM1865XXUT/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2950WXZR](/measurement-sets/IGVFDS2950WXZR/) 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/IGVFDS2950WXZR/"
}
]
},
"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"
},
"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"
}
],
"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": "2023-11-30T22:48:21.472977+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": [
{
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"accession": "IGVFFI1827IVYF",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinD-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:35:22.087776+00:00",
"file_format": "fastq",
"file_size": 7700910,
"href": "/sequence-files/IGVFFI1827IVYF/@@download/IGVFFI1827IVYF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e3fb597f-53ec-4f07-80b3-cfc83834a477/IGVFFI1827IVYF.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_S17-BioRep3-FFRep1-BinD-PCRrep1_S144_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3995GHXU/",
"accession": "IGVFFI3995GHXU",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinD-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:52:13.067737+00:00",
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"file_size": 3415625,
"href": "/sequence-files/IGVFFI3995GHXU/@@download/IGVFFI3995GHXU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b10a3c3b-3bb3-4696-bd87-def57d39dbf1/IGVFFI3995GHXU.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_S17-BioRep3-FFRep1-BinD-PCRrep1_S144_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7134JKWO/",
"accession": "IGVFFI7134JKWO",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinD-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:43:48.441874+00:00",
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"file_size": 14213811,
"href": "/sequence-files/IGVFFI7134JKWO/@@download/IGVFFI7134JKWO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/3b9d39af-c805-4bb1-9de8-c26940e37eb7/IGVFFI7134JKWO.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_S17-BioRep3-FFRep1-BinD-PCRrep1_S144_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9482QSDK/",
"accession": "IGVFFI9482QSDK",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinD-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:33:39.304200+00:00",
"file_format": "fastq",
"file_size": 3156255,
"href": "/sequence-files/IGVFFI9482QSDK/@@download/IGVFFI9482QSDK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/65a626db-c0d1-46f2-9dc7-338dc7ef90f2/IGVFFI9482QSDK.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NextSeq 550"
},
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5885CAZU/",
"accession": "IGVFFI5885CAZU",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinD-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:25:26.192441+00:00",
"file_format": "fastq",
"file_size": 3304072,
"href": "/sequence-files/IGVFFI5885CAZU/@@download/IGVFFI5885CAZU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/076ee20d-f61f-42ef-a36f-1c517f05f0c5/IGVFFI5885CAZU.fastq.gz",
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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_S17-BioRep3-FFRep1-BinD-PCRrep2_S201_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1585CPUX/",
"accession": "IGVFFI1585CPUX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinD-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:08:33.498134+00:00",
"file_format": "fastq",
"file_size": 7573398,
"href": "/sequence-files/IGVFFI1585CPUX/@@download/IGVFFI1585CPUX.fastq.gz",
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"term_name": "Illumina NextSeq 550"
},
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"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S17-BioRep3-FFRep1-BinD-PCRrep2_S201_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0675ERAV/",
"accession": "IGVFFI0675ERAV",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinD-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
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"term_name": "Illumina NextSeq 550"
},
"status": "released",
"submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S17-BioRep3-FFRep1-BinD-PCRrep2_S201_R2_001.fastq.gz",
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},
{
"@id": "/sequence-files/IGVFFI0786VNUG/",
"accession": "IGVFFI0786VNUG",
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],
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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_S17-BioRep3-FFRep1-BinD-PCRrep1_S144_I2_001.fastq.gz",
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}
],
"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": "2023-12-20T23:04:39.615699+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1865XXUT/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1865XXUT",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinD"
],
"classifications": [
"cell line"
],
"institutional_certificates": [],
"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": "Homo sapiens (male) Jurkat cell line (sorting details: FACS bin for 55-65% 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), transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens",
"treatments": [
{
"@id": "/treatments/df02c0d4-f796-4f77-bfbc-388cdbfcc615/",
"purpose": "stimulation",
"status": "released",
"summary": "Treatment of 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours",
"treatment_type": "protein"
},
{
"@id": "/treatments/42b3c61d-38de-4bd2-bb39-33c125a417cb/",
"purpose": "stimulation",
"status": "released",
"summary": "Treatment of 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours",
"treatment_type": "chemical"
}
]
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T19:35:22.087776+00:00",
"summary": "CRISPR prime editing Variant-EFFECTS sorted on the expression of PPIF 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": [
"PPIase F",
"peptidylprolyl isomerase F",
"Cyp-D",
"peptidyl-prolyl cis-trans isomerase F, mitochondrial",
"PPIF",
"CyP-M",
"cyclophilin F",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"cyclophilin 3",
"cyclophilin D",
"rotamase F",
"mitochondrial cyclophilin",
"CypD",
"CYP3"
]
}
],
"uuid": "b1cda975-73a4-47dd-a1b7-93c6b6f20e75"
}