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| Status |
Public on Jan 03, 2011 |
| Title |
Small RNA sequencing in mouse cardiomyocytes after siRNA mediated knockdown of Srf |
| Organism |
Mus musculus |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
We performed two independent siRNA mediated knockdowns of Srf (Srf si1 & Srf si2) and an unspecific siRNA (siNon) in mouse cardiomyocytes HL-1 cells. Small RNAs were sequenced by Illumina/Solexa next-generation (single-end) sequencing technology. The sequence reads were mapped to the mouse reference genome (NCBI v37, mm9) using MicroRazerS. MicroRazerS searches for the longest possible prefix-match of each read, i.e. the longest possible contiguous match starting at the first base. Hence, it is robust to possible adapter sequence at the 3' end of a read and requires no adapter trimming.
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| |
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| Overall design |
Small RNA-seq profiles of two siRNA mediated knockdowns of Srf and an unspecific siRNA in mouse cardiomyocytes
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| |
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| Contributor(s) |
Sperling SR |
| Citation(s) |
21379568 |
| Submission date |
Nov 17, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Silke Sperling |
| E-mail(s) |
silke.sperling@charite.de
|
| Phone |
++49 (0)30 450540123
|
| Organization name |
Experimental and Clinical Research Center (ECRC), Charité / MDC for Molecular Medicine
|
| Department |
Cardiovascular Genetics
|
| Lab |
Cardiovascular Genetics
|
| Street address |
Lindenberger Weg 80
|
| City |
Berlin |
| State/province |
Berlin |
| ZIP/Postal code |
13125 |
| Country |
Germany |
| |
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| Platforms (1) |
| GPL9185 |
Illumina Genome Analyzer (Mus musculus) |
|
| Samples (3) |
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| This SubSeries is part of SuperSeries: |
| GSE26397 |
The Cardiac Transcription Network Modulated by Gata4, Mef2a, Nkx2.5 and Srf, Histone Modifications and MicroRNAs |
|
| Relations |
| SRA |
SRP002213 |
| BioProject |
PRJNA141689 |
