Comparison of PPIH knockdown in HeLa cells compared to scrambled shRNA control
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE103648 | GEO | 2017/12/31
SECONDARY ACCESSION(S): PRJNA403845
REPOSITORIES: GEO
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Project description:HEK293T cells transduced with shRNA from MISSION library TRCN0000049326 using lentiviral delivery system. HEK293T cells transduced with scrambled shRNA, gifted from Dr. Mauricio Reginato. Tara L Davis, S. RaElle Jackson, Beth Adams, Anh Trinh performed primary experimental contributions to cell lines, RNA/cDNA preparation, and validations, all Drexel University College of Medicine, Philadelphia, PA. Hetty Rodriguez and John Tobias performed Bioanalyzer and microarray expreriments, and initial data processing. Affiliation: Molecular Profiling Facility and Genomic Analysis Core Bioinformatics Group, University of Pennsylvania, Philadelphia, PA. Human PPIG (alias: SR-Cyp, CARS) is a cyclophilin, an enzyme that interconverts cis and trans isomers of proline. The PPIG gene, in addition to the cyclophilin domain, encodes for a multiple C-terminal SR motifs. PPIG associates with the human spliceosome, the complex and dynamic machinery that removes intronic sequence from pre-messenger RNA (pre-mRNA). Nothing is known about the function of PPIG in regulation of alternative splicing. To understand the function of PPIG, we knocked down PPIG in human cells. We characterized a set of alternative splicing and transcriptional events that are PPIG-responsive. We used these splicing and transcriptional bioassays to show that PPIG-responsive events are largely specific, even within the cyclophilin family.
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Project description:HEK293T cells transduced with shRNA from MISSION library TRCN0000049368 using lentiviral delivery system. HEK293T cells transduced with scrambled shRNA, gifted from Dr. Mauricio Reginato. Tara L Davis, S. RaElle Jackson, Beth Adams, Anh Trinh, and Jennifer Ayoub performed primary experimental contributions to cell lines, RNA/cDNA preparation, and validation, all Drexel University College of Medicine, Philadelphia, PA. Hetty Rodriguez and John Tobias performed Bioanalyzer and microarray expreriments, and initial data processing. Affiliation: Molecular Profiling Facility and Genomic Analysis Core Bioinformatics Group, University of Pennsylvania, Philadelphia, PA. Human PPIE is a cyclophilin, an enzyme that interconverts cis and trans isomers of proline. The PPIE gene, in addition to the cyclophilin domain, encodes for an N-terminal RRM. PPIE associates with the human spliceosome, the complex and dynamic machinery that removes intronic sequence from pre-messenger RNA (pre-mRNA). Nothing is known about the function of PPIE in regulation of alternative splicing, although it has been shown to modulate chromatin modification. To further understand the function of PPIE, we knocked down PPIE in human cells. We characterized a set of alternative splicing and transcriptional events that are PPIE-responsive. We used these splicing and transcriptional bioassays to show that PPIE-responsive events are largely specific, even within the cyclophilin family.
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Project description:HEK293T cells transduced with shRNA from MISSION library TRCN0000230475 using lentiviral delivery system. HEK293T cells transduced with scrambled shRNA, gifted from Dr. Mauricio Reginato. Tara L Davis, S. RaElle Jackson, Beth Adams, Anh Trinh, Tracey Yenailtus, Jessica Kopenhaver, Angie Giang, and Alyson Hurlock performed primary experimental contributions to cell lines, RNA/cDNA preparation, and validation, all Drexel University College of Medicine, Philadelphia, PA. Hetty Rodriguez and John Tobias performed Bioanalyzer and microarray expreriments, and initial data processing. Affiliation: Molecular Profiling Facility and Genomic Analysis Core Bioinformatics Group, University of Pennsylvania, Philadelphia, PA. Human PPIL2 is a cyclophilin, an enzyme that interconverts cis and trans isomers of proline. The PPIL2 gene, in addition to the cyclophilin domain, encodes for an N-terminal U-box motif. PPIL2 associates with the human spliceosome, the complex and dynamic machinery that removes intronic sequence from pre-messenger RNA (pre-mRNA). Nothing is known about the function of PPIL2 in regulation of alternative splicing, although it has been shown to modulate transcription of a handful of targets, albeit indirectly. To further understand the function of PPIL2, we knocked down PPIL2 in human cells. We characterized a set of alternative splicing and transcriptional events that are PPIL2-responsive. We used these splicing and transcriptional bioassays to show that PPIL2-responsive events are largely specific, even within the cyclophilin family.
2018-10-01 | GSE117373 | GEO
Project description:HEK293T cells transduced with shRNA from MISSION library TRCN0000000139 using lentiviral delivery system. HEK293T cells transduced with scrambled shRNA, gifted from Dr. Mauricio Reginato. Sequence is 5′-CCTAAGGTTAAGTCGCCCTCGCTCTAGCGAGGGCGACTTAACCTT-3′. Tara L Davis, S. RaElle Jackson, Beth Adams, Anh Trinh, Peter Naranjo, and Angie Giang performed primary experimental contributions to cell lines, RNA/cDNA preparation, and validation of results, all Drexel University College of Medicine, Philadelphia, PA 19102. Hetty Rodriguez and John Tobias performed Bioanalyzer and microarray expreriments, and initial data processing. Affiliation: Molecular Profiling Facility and Genomic Analysis Core Bioinformatics Group, University of Pennsylvania. Human CWC27 (aliases: NY-CO-10, Serologically Defined Colon Cancer Antigen 10 or SDCCAG-10) is a cyclophilin, an enzyme that interconverts cis and trans isomers of proline. The CWC27 gene, in addition to the cyclophilin domain, encodes for two low complexity regions and a coiled coil region. CWC27 associates with the human spliceosome, the complex and dynamic machinery that removes intronic sequence from pre-messenger RNA (pre-mRNA). Nothing is known about the function of CWC27 in the nucleus. To understand the function of CWC27, we knocked down CWC27 in human cells. We characterized a set of alternative splicing and transcriptional events that are CWC27-responsive. We used these splicing and transcriptional bioassays to show that CWC27-responsive events are largely specific, even within the cyclophilin family.
2018-10-01 | GSE117144 | GEO
Project description:HEK293T cells transduced with two shRNAs from MISSION library (TRCN0000364755 and TRCN0000074769) using lentiviral delivery system. HEK293T cells transduced with scrambled shRNA, gifted from Dr. Mauricio Reginato. Sequence is 5′-CCTAAGGTTAAGTCGCCCTCGCTCTAGCGAGGGCGACTTAACCTT-3′. Primary contributions to creation of cell lines, preparation of RNA/cDNA for microarray, and validation of results were from Tara L Davis, S. RaElle Jackson, Beth Adams, Anh Trinh, Nicholas Fox, Jessica Kopenhaver, Alyson Hurlock, and Achraf Jardaly, all Drexel University College of Medicine, Philadephia PA, 19102. Hetty Rodriguez and John Tobias, affiliated with the Molecular Profiling Facility and Genomic Analysis Core Bioinformatics Group at the University of Pennsylvania, Philadelphia PA, performed Bioanalyzer and microarray expreriments and initial data processing. pre-mRNA Processing Factor 4 (PRPF4) is a scaffolding protein, consisting of two N-terminal intrinsically disordered motifs and a C-terminal WD-40 domain. PRPF4 associates with the human spliceosome, the complex and dynamic machinery that removes intronic sequence from pre-messenger RNA (pre-mRNA). Although PRPF4 affects the ability of the spliceosome to assemble and catalyze splicing in vitro through de-stabilization of the tri-snRNP complex, little is known about what PRPF4 does to regulate transcription and splicing in vivo. To understand the function of PRPF4 in the nucleus, we knocked down PRPF4 in human cells. We characterized a set of alternative splicing and transcriptional events that are PRPF4-responsive. We used these splicing and transcriptional bioassays to show that PRPF4-responsive events are largely specific. The development of a bioassay for PRPF4 function can be used to answer fundamental questions about the role of spliceosomal proteins in regulating splicing and other nuclear functions.
2018-10-01 | GSE117384 | GEO
Project description:HEK293T cells transduced with two shRNAs from MISSION library (TRCN0000180560 and TRCN0000148198) using lentiviral delivery system. HEK293T cells transduced with scrambled shRNA, gifted from Dr. Mauricio Reginato. Sequence is 5′-CCTAAGGTTAAGTCGCCCTCGCTCTAGCGAGGGCGACTTAACCTT-3′. Primary contributions to creation of cell lines, preparation of RNA/cDNA for microarray, and validation of results were from Tara L Davis, S. RaElle Jackson, Beth Adams, Anh Trinh, Jessica Kopenhaver, Alyson Hurlock, Angie Giang, and Purva Vaidya, all Drexel University College of Medicine, Philadephia PA, 19102. Hetty Rodriguez and John Tobias, affiliated with the Molecular Profiling Facility and Genomic Analysis Core Bioinformatics Group at the University of Pennsylvania, Philadelphia PA, performed Bioanalyzer and microarray expreriments and initial data processing. Zinc Finger 830 (ZNF830) is a scaffolding protein, consisting of an N-terminal C2H2 zinc finger motif and a C-terminal domain of unknown function (DUF). ZNF830 associates with the human spliceosome, the complex and dynamic machinery that removes intronic sequence from pre-messenger RNA (pre-mRNA). Although ZNF830 knockdown in mice is lethal due to cell cycle defects, a common phenotype for regulators of alternative splicing, little is known about the targets of ZNF830 transcription and splicing regulation in human cells. To understand the function of ZNF830 in the nucleus, we knocked down ZNF830 in human cells. We characterized a set of alternative splicing and transcriptional events that are ZNF830-responsive. We used these splicing and transcriptional bioassays to show that ZNF830-responsive events are largely specific. The development of a bioassay for ZNF830 function can be used to answer fundamental questions about the role of spliceosomal proteins in regulating splicing and other nuclear functions.
2018-10-01 | GSE117390 | GEO
Project description:Somatic mutations in the spliceosome gene ZRSR2 (located on the X chromosome) are associated with myelodysplastic syndrome (MDS). ZRSR2 is involved in the recognition of 3' splice site during the early stages of spliceosome assembly; however, its precise role in RNA splicing has remained unclear. Here, we characterize ZRSR2 as an essential component of the minor spliceosome (U12-dependent) assembly. shRNA mediated knockdown of ZRSR2 leads to impaired splicing of the U12-type introns, and RNA-Sequencing of MDS bone marrow reveals that loss of ZRSR2 activity causes increased mis-splicing. These splicing defects involve retention of the U12-type introns while splicing of the U2-type introns remain mostly unaffected. ZRSR2 deficient cells also exhibit reduced proliferation potential and distinct alterations in myeloid and erythroid differentiation in vitro. These data identify a specific role for ZRSR2 in RNA splicing and highlight dysregulated splicing of U12-type introns as a characteristic feature of ZRSR2 mutations in MDS. RNA sequencing was performed on 16 bone marrow samples (MDS and normal) and six samples of control or ZRSR2 shRNA transduced TF-1 cells and data was analysed for aberrant splicing caused by ZRSR2 mutations/deficiency.
2015-01-15 | E-GEOD-63816 | biostudies-arrayexpress