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Series GSE117376 Query DataSets for GSE117376
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
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.
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
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
Submission date Jul 19, 2018
Last update date May 15, 2019
Contact name Tara Davis
Organization name Drexel University College of Medicine
Department Biochemistry and Molecular Biology
Lab Lab 10127
Street address 245 N. 15th St. MS 497
City Philadelphia
State/province PA
ZIP/Postal code 19102
Country USA
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]
Samples (12)
GSM3293566 HEK293T_5191SCR_gene_rep1
GSM3293567 HEK293T_5191SCR_gene_rep2
GSM3293568 HEK293T_5191SCR_gene_rep3
BioProject PRJNA481942

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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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