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| Status |
Public on Dec 01, 2015 |
| Title |
PARP-1 regulation of alternative splicing |
| Organism |
Drosophila melanogaster |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
To address the global impact of PARP-1 on alternative splicing, we isolated total RNA in two biological replicates from control (non-treated), PARP-1 siRNA- and PJ-34-treated cells. Sequencing of these RNAs on an Illumina HiSeq 2500, yielded >56 million 100-bp paired-end RNA-seq reads. First we tested if PARP-1 KD was effective at the RNA-seq level. Read aligning to the entire gene body of PARP-1 shown a reduction in PARP-1 expression of about 1.5-fold (P-value < 0.0003), confirming that indeed PARP-1 was depleted after PARP-1 siRNA treatment. We next used these RNA-seq data sets (control, PARP-1 KD and PARylation inhibited) to assess whether these treatments resulted in changes in i) gene expression and ii) alternative splicing.
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| |
|
| Overall design |
mRNA profiles of two biological replicates (non-treated), two PARP-1 siRNA knockdowns (100ng and 500ng) and two PARylation inhibition PJ-34-treated cells (10uM and 0.3uM) were compared using RNA-Seq on an Illumina HiSeq 2500.
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| |
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| Contributor(s) |
Matveeva E, Maiorano J, Zhang Q, Eteleeb AM, Convertini P, Rouchka EC, Stamm S, Wang J, Fondufe-Mittendorf Y |
| Citation(s) |
27462443 |
| |
| Submission date |
Mar 20, 2014 |
| Last update date |
Jul 24, 2019 |
| Contact name |
Eric Christian Rouchka |
| E-mail(s) |
eric.rouchka@louisville.edu
|
| Organization name |
University of Louisville
|
| Department |
Biochemistry and Molecular Genetics
|
| Lab |
KY INBRE Bioinformatics Core
|
| Street address |
522 East Gray Street
|
| City |
Louisville |
| State/province |
Kentucky |
| ZIP/Postal code |
40292 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL17275 |
Illumina HiSeq 2500 (Drosophila melanogaster) |
|
| Samples (6)
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| Relations |
| BioProject |
PRJNA242341 |
| SRA |
SRP040420 |
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