{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2784BXPD/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2784BXPD",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinF_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 [IGVFDS2784BXPD](/measurement-sets/IGVFDS2784BXPD/) has sequence file(s) [IGVFFI7313ABVS](/sequence-files/IGVFFI7313ABVS/), [IGVFFI1568SJFQ](/sequence-files/IGVFFI1568SJFQ/), [IGVFFI0689VGEW](/sequence-files/IGVFFI0689VGEW/), [IGVFFI7622AGUZ](/sequence-files/IGVFFI7622AGUZ/), [IGVFFI2221JBFX](/sequence-files/IGVFFI2221JBFX/), [IGVFFI6711FHWN](/sequence-files/IGVFFI6711FHWN/), [IGVFFI8572WCPP](/sequence-files/IGVFFI8572WCPP/), [IGVFFI2973ZTDF](/sequence-files/IGVFFI2973ZTDF/) 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/IGVFDS2784BXPD/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2784BXPD](/measurement-sets/IGVFDS2784BXPD/) has sequence file(s): [IGVFFI7313ABVS](/sequence-files/IGVFFI7313ABVS/), [IGVFFI1568SJFQ](/sequence-files/IGVFFI1568SJFQ/), [IGVFFI0689VGEW](/sequence-files/IGVFFI0689VGEW/), [IGVFFI7622AGUZ](/sequence-files/IGVFFI7622AGUZ/), [IGVFFI2221JBFX](/sequence-files/IGVFFI2221JBFX/), [IGVFFI6711FHWN](/sequence-files/IGVFFI6711FHWN/), [IGVFFI8572WCPP](/sequence-files/IGVFFI8572WCPP/), [IGVFFI2973ZTDF](/sequence-files/IGVFFI2973ZTDF/) 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/IGVFDS2784BXPD/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM6938ZJAF](/in-vitro-systems/IGVFSM6938ZJAF/) 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/IGVFSM6938ZJAF/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2784BXPD](/measurement-sets/IGVFDS2784BXPD/) 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/IGVFDS2784BXPD/"
}
]
},
"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": "2023-11-30T22:47:51.344933+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": "IGVFFI7313ABVS",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinF-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:56:34.179507+00:00",
"file_format": "fastq",
"file_size": 2981191,
"href": "/sequence-files/IGVFFI7313ABVS/@@download/IGVFFI7313ABVS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/39008ac4-9c6c-485f-8408-1a4f268e5629/IGVFFI7313ABVS.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-BinF-PCRrep1_S118_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1568SJFQ/",
"accession": "IGVFFI1568SJFQ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinF-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:04:42.293782+00:00",
"file_format": "fastq",
"file_size": 7370604,
"href": "/sequence-files/IGVFFI1568SJFQ/@@download/IGVFFI1568SJFQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/11358e7f-51cb-4d89-a7b1-176461fd5d96/IGVFFI1568SJFQ.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-BinF-PCRrep2_S175_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0689VGEW/",
"accession": "IGVFFI0689VGEW",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinF-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:21:31.578047+00:00",
"file_format": "fastq",
"file_size": 3271842,
"href": "/sequence-files/IGVFFI0689VGEW/@@download/IGVFFI0689VGEW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/3704ae3e-0617-4eff-908d-35d5b0b5a9f5/IGVFFI0689VGEW.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-BinF-PCRrep2_S175_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7622AGUZ/",
"accession": "IGVFFI7622AGUZ",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinF-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:29:51.782249+00:00",
"file_format": "fastq",
"file_size": 3091708,
"href": "/sequence-files/IGVFFI7622AGUZ/@@download/IGVFFI7622AGUZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b3ca4fbf-ae3e-4f51-83cb-de480bfea568/IGVFFI7622AGUZ.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-BinF-PCRrep2_S175_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2221JBFX/",
"accession": "IGVFFI2221JBFX",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinF-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:48:22.151347+00:00",
"file_format": "fastq",
"file_size": 3206142,
"href": "/sequence-files/IGVFFI2221JBFX/@@download/IGVFFI2221JBFX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/686df6d2-b97b-4a79-94fb-eb2c3da1350b/IGVFFI2221JBFX.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_S12-BioRep1-FFRep1-BinF-PCRrep1_S118_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6711FHWN/",
"accession": "IGVFFI6711FHWN",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinF-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:39:49.757994+00:00",
"file_format": "fastq",
"file_size": 13213548,
"href": "/sequence-files/IGVFFI6711FHWN/@@download/IGVFFI6711FHWN.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/0e7fc84e-cf53-4e41-a2f8-f17b47e269f7/IGVFFI6711FHWN.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_S12-BioRep1-FFRep1-BinF-PCRrep1_S118_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8572WCPP/",
"accession": "IGVFFI8572WCPP",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinF-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:31:28.715755+00:00",
"file_format": "fastq",
"file_size": 7076024,
"href": "/sequence-files/IGVFFI8572WCPP/@@download/IGVFFI8572WCPP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/55ec9e33-2b96-4b28-a52c-6a0eadd64026/IGVFFI8572WCPP.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_S12-BioRep1-FFRep1-BinF-PCRrep1_S118_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2973ZTDF/",
"accession": "IGVFFI2973ZTDF",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinF-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:13:01.058079+00:00",
"file_format": "fastq",
"file_size": 13795239,
"href": "/sequence-files/IGVFFI2973ZTDF/@@download/IGVFFI2973ZTDF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/21cc3f34-621f-4111-8d9c-23955c8b0904/IGVFFI2973ZTDF.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-BinF-PCRrep2_S175_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": "2023-12-20T23:03:37.902398+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM6938ZJAF/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6938ZJAF",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinF"
],
"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 90-100% 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": "2023-12-05T19:31:28.715755+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": "81c80c33-c7a0-4fd8-9002-ff8cd513f444"
}