Comparison of PPIG knockdown in HEK293T cells compared to scrambled shRNA control
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE117234 | GEO | 2018/10/01
REPOSITORIES: GEO
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Project description:HEK293T cells transduced with shRNA from MISSION library TRCN0000420470 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, Jenna Marinock, Peter Naranjo, NIcholas Fox, and Gueil Wong-Shing 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 PPIL1 is a cyclophilin, an enzyme that interconverts cis and trans isomers of proline. PPIL1 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 PPIL1 in regulating transcription or alternative splicing events. To understand the nuclear function of PPIL1, we knocked down PPIL1 in human cells. We characterized a set of alternative splicing and transcriptional events that are PPIL1-responsive. We used these splicing and transcriptional bioassays to show that PPIL1-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 TRCN0000000185 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, Jonathan Amora, Peter Naranjo, Gueil Wong-Shing, and Nii Martey 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 PPIL3 is a cyclophilin, an enzyme that interconverts cis and trans isomers of proline. PPIL3 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 PPIL3 in the nucleus. To understand the function of PPIL3, we knocked down PPIL3 in human cells. We characterized a set of alternative splicing and transcriptional events that are PPIL3-responsive. We used these splicing and transcriptional bioassays to show that PPIL3-responsive events are largely specific, even within the cyclophilin family.
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Project description:HEK293T cells transduced with shRNA from MISSION library TRCN0000000165 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, Jenna Marinock, 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 PPWD1 is a cyclophilin, an enzyme that interconverts cis and trans isomers of proline. The PPWD1 gene, in addition to the cyclophilin domain, encodes for an N-terminal WD40 domain. PPWD1 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 PPWD1 in regulation of nuclear events. To further understand the function of PPWD1, we knocked down PPWD1 in human cells. We characterized a set of alternative splicing and transcriptional events that are PPWD1-responsive. We used these splicing and transcriptional bioassays to show that PPWD1-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.
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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.
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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.
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Project description:HeLa cells transduced with shRNA from MISSION library (TRCN0000289677) using lentiviral delivery system. HeLa cells transduced with scrambled shRNA, gifted from Dr. Mauricio Reginato. Sequence is 5′-CCTAAGGTTAAGTCGCCCTCGCTCTAGCGAGGGCGACTTAACCTT-3′ Peptidyl-prolyl isomerase H (PPIH) is a cyclophilin, an enzyme that interconverts cis and trans isomers of proline. PPIH associates with the human spliceosome, the complex and dynamic machinery that removes intronic sequence from pre-messenger RNA (pre-mRNA). Although PPIH affects the ability of the spliceosome to assemble and catalyze splicing in vitro, little is known about what PPIH does to splicing in vivo. To understand the function of PPIH in the nucleus, we knocked down PPIH in human cells. We characterized a set of alternative splicing and transcriptional events that are PPIH-responsive. We used these splicing and transcriptional bioassays to show first that PPIH-responsive events are largely specific, even within the cyclophilin family. We then identified a role for proline isomerization in transcriptional regulation, but not in regulation of alternative splicing. The development of a bioassay for PPIH function can be used to answer fundamental questions about the role of spliceosomal proteins in regulating splicing and other nuclear functions.
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2012-08-17 | E-GEOD-37731 | biostudies-arrayexpress