{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6022UUBF/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6022UUBF",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-BinB_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 [IGVFDS6022UUBF](/measurement-sets/IGVFDS6022UUBF/) has sequence file(s) [IGVFFI4391PCQD](/sequence-files/IGVFFI4391PCQD/), [IGVFFI2377SYTW](/sequence-files/IGVFFI2377SYTW/), [IGVFFI7835QFFT](/sequence-files/IGVFFI7835QFFT/), [IGVFFI6495WAOH](/sequence-files/IGVFFI6495WAOH/), [IGVFFI0956JLMD](/sequence-files/IGVFFI0956JLMD/), [IGVFFI0704XIHD](/sequence-files/IGVFFI0704XIHD/), [IGVFFI2575CMLO](/sequence-files/IGVFFI2575CMLO/), [IGVFFI6776LNJP](/sequence-files/IGVFFI6776LNJP/) 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/IGVFDS6022UUBF/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS6022UUBF](/measurement-sets/IGVFDS6022UUBF/) has sequence file(s): [IGVFFI4391PCQD](/sequence-files/IGVFFI4391PCQD/), [IGVFFI2377SYTW](/sequence-files/IGVFFI2377SYTW/), [IGVFFI7835QFFT](/sequence-files/IGVFFI7835QFFT/), [IGVFFI6495WAOH](/sequence-files/IGVFFI6495WAOH/), [IGVFFI0956JLMD](/sequence-files/IGVFFI0956JLMD/), [IGVFFI0704XIHD](/sequence-files/IGVFFI0704XIHD/), [IGVFFI2575CMLO](/sequence-files/IGVFFI2575CMLO/), [IGVFFI6776LNJP](/sequence-files/IGVFFI6776LNJP/) 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/IGVFDS6022UUBF/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM5179ONAU](/in-vitro-systems/IGVFSM5179ONAU/) 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/IGVFSM5179ONAU/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS6022UUBF](/measurement-sets/IGVFDS6022UUBF/) 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/IGVFDS6022UUBF/"
}
]
},
"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": "2023-11-30T22:48:34.683542+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/IGVFFI4391PCQD/",
"accession": "IGVFFI4391PCQD",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-BinB-PCRrep1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:53:57.607303+00:00",
"file_format": "fastq",
"file_size": 3153846,
"href": "/sequence-files/IGVFFI4391PCQD/@@download/IGVFFI4391PCQD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/f20adf1a-bff8-4ac2-a3b3-86cc72092522/IGVFFI4391PCQD.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-BinB-PCRrep1_S156_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2377SYTW/",
"accession": "IGVFFI2377SYTW",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-BinB-PCRrep2_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:35:24.082938+00:00",
"file_format": "fastq",
"file_size": 3281559,
"href": "/sequence-files/IGVFFI2377SYTW/@@download/IGVFFI2377SYTW.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/680e418c-6ce6-49f5-9667-ceae041e0865/IGVFFI2377SYTW.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-BinB-PCRrep2_S213_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7835QFFT/",
"accession": "IGVFFI7835QFFT",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-BinB-PCRrep2_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:27:11.064104+00:00",
"file_format": "fastq",
"file_size": 3339019,
"href": "/sequence-files/IGVFFI7835QFFT/@@download/IGVFFI7835QFFT.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/133d1877-5131-4ce5-8ba8-c95deffa2dc1/IGVFFI7835QFFT.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-BinB-PCRrep2_S213_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6495WAOH/",
"accession": "IGVFFI6495WAOH",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-BinB-PCRrep1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:37:08.543444+00:00",
"file_format": "fastq",
"file_size": 7385816,
"href": "/sequence-files/IGVFFI6495WAOH/@@download/IGVFFI6495WAOH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/bba8a287-1c7b-4694-8976-7c6fa3d68349/IGVFFI6495WAOH.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-BinB-PCRrep1_S156_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0956JLMD/",
"accession": "IGVFFI0956JLMD",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-BinB-PCRrep2_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:18:49.128090+00:00",
"file_format": "fastq",
"file_size": 14498368,
"href": "/sequence-files/IGVFFI0956JLMD/@@download/IGVFFI0956JLMD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/7d3f684f-d4b9-49fc-aba3-01a06fa98c90/IGVFFI0956JLMD.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-BinB-PCRrep2_S213_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0704XIHD/",
"accession": "IGVFFI0704XIHD",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-BinB-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:02:05.054398+00:00",
"file_format": "fastq",
"file_size": 3071910,
"href": "/sequence-files/IGVFFI0704XIHD/@@download/IGVFFI0704XIHD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/e2d08ebc-115f-4f0d-a1fc-f6af6f026385/IGVFFI0704XIHD.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-BinB-PCRrep1_S156_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2575CMLO/",
"accession": "IGVFFI2575CMLO",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-BinB-PCRrep2_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T20:10:19.975868+00:00",
"file_format": "fastq",
"file_size": 7874354,
"href": "/sequence-files/IGVFFI2575CMLO/@@download/IGVFFI2575CMLO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/a69c3d2d-5bba-42e0-85b8-e5187521ae0a/IGVFFI2575CMLO.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-BinB-PCRrep2_S213_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6776LNJP/",
"accession": "IGVFFI6776LNJP",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-BinB-PCRrep1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-05T19:45:38.247435+00:00",
"file_format": "fastq",
"file_size": 13436789,
"href": "/sequence-files/IGVFFI6776LNJP/@@download/IGVFFI6776LNJP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/05/b087086b-c2d8-4ed4-9ac6-f7f9116f0e0a/IGVFFI6776LNJP.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-BinB-PCRrep1_S156_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": "2023-12-20T23:05:10.578782+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5179ONAU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5179ONAU",
"aliases": [
"jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-BinB"
],
"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 11-20% 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": "2023-12-05T19:37:08.543444+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": "8b385326-3978-4a5a-b3c7-2e772d61d2a4"
}