C2C12 were transfected with 30 nM of Mef2a siRNA-2 or scrambled control and RNA was then isolated at 48 h DM, as described above, in duplicate. A total of 5 μg of purified RNA was delivered to McGill University and Genome Quebec Innovation Centre (MUGQIC) for cDNA library preparation (Illumina TruSeq mRNA sample preparation kit), RNA-sequencing (Illumina HiSeq 2000; 100 bp paired-end reads; 4 samples per lane) and bioinformatic analysis. The bioinformatic pipeline included Illumina CASAVA software, Trimmomatic (40 (link)), and TopHat/Bowtie (41 (link)). Sequencing reads were aligned to the mm10 genome assembly. HTSeq-count generated raw read counts which were used to identify differentially expressed genes using edgeR (42 (link)) and DESeq (43 (link)).
Protocol detail
RNA-seq analysis of Mef2a knockdown
Partial Protocol Preview
This section provides a glimpse into the protocol.
The remaining content is hidden due to licensing restrictions, but the full text is available at the following link:
Access Free Full Text.
Corresponding Organization :
Other organizations : York University, University of Ottawa
Top 5 similar protocols
Protocol cited in 3 other protocols
Variable analysis
independent variables
- Mef2a siRNA-2
- Scrambled control
- RNA expression
- C2C12 cell line
- 48 h DM (differentiation medium)
- Illumina TruSeq mRNA sample preparation kit
- Illumina HiSeq 2000 (100 bp paired-end reads, 4 samples per lane)
- Bioinformatic pipeline (Illumina CASAVA, Trimmomatic, TopHat/Bowtie)
- Alignment to mm10 genome assembly
- HTSeq-count raw read counts
- Differential expression analysis (edgeR, DESeq)
- scrambled control
Annotations
Based on most similar protocols
Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.
Sign up for free or login to display all annotations
As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!