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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 01, 2018 |
| Title |
Comparison of PPWD1 knockdown in HEK293T cells compared to scrambled shRNA control |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
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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| Overall design |
3 replicates of PPWD1 knockdown cell lines (HEK293T cells, stably integrated, selected using puro, MISSION shRNA (TRCN0000000165, 5'-CCGGGCTTAGGACTTGCTGAATATACTCGAGTATATTCAGCAAGTCCTAAGCTTTTT-3'). 3 replicates of SCR control cells lines (HEK293T cells, stably integrated, selected using puro, sequence 5′-CCTAAGGTTAAGTCGCCCTCGCTCTAGCGAGGGCGACTTAACCTT-3′). total RNA purified from ~1 million cells, cDNA converted using random hexamer primers, quantity measured using NanoDrop, quality quantified using BioAnaylzer. Affymatrix HTA2.0 array
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| Contributor(s) |
Davis TL, Jackson SR, Adams B, Trinh A, Marinock J, Ayoub J, Rodriguez H, Tobias J |
| Citation(s) |
30518120 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R00 GM094293 |
Functional and structural characterization of spliceosomal cyclophilins |
DREXEL UNIVERSITY |
Tara L Davis |
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| Submission date |
Jul 19, 2018 |
| Last update date |
May 15, 2019 |
| Contact name |
Tara Davis |
| E-mail(s) |
Tara.Davis@DrexelMed.edu
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| Organization name |
Drexel University College of Medicine
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| Department |
Biochemistry and Molecular Biology
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| Lab |
Lab 10127
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| Street address |
245 N. 15th St. MS 497
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19102 |
| Country |
USA |
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| Platforms (2) |
| GPL17585 |
[HTA-2_0] Affymetrix Human Transcriptome Array 2.0 [probe set (exon) version] |
| GPL17586 |
[HTA-2_0] Affymetrix Human Transcriptome Array 2.0 [transcript (gene) version] |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA481942 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE117376_RAW.tar |
375.4 Mb |
(http)(custom) |
TAR (of CEL, CHP) |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
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