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| Status |
Public on Oct 01, 2018 |
| Title |
Comparison of PPIL1 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 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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| Overall design |
3 replicates of PPIL1 knockdown cell lines (HEK293T cells, stably integrated, selected using puro, MISSION shRNA (TRCN0000420470, 5'-CCGGTACTACACATGAACCATAATGCTCGAGCATTATGGTTCATGTGTAGTATTTTTTG-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, Wong-Shing G, Naranjo P, Fox N, Rodriguez H, Tobias J |
| Citation(s) |
30518120 |
| 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 |
PRJNA481959 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE117381_RAW.tar |
374.7 Mb |
(http)(custom) |
TAR (of CEL, CHP) |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
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