Ransom Library prep for GC-rich genes

[anne-lyse]

Hi,
We would like to do differential expression analysis, we did a genome (Illumina + PacBIo) and a transcriptome (Kapa mRNA kit) but GC-rich genes are missing.
What is the best library prep for GC-rich genes? I am working with birds and some genes have a GC-content above 70%?
We are interested in genes which have low expression levels, apparently the rRNA depletion will not work well for our non-model organism (http://www.epibio.com/rnamatchmaker). What will you use?
Thank you for your answer.
Anne-Lyse

[nucacidhunter]

1- GC rich sequences are inefficient in amplification step. You can use one of polymerases that are more efficient in amplifying GC rich sequences instead of supplied polymerase with kit you are using. A literature search might narrow down effective brands.

2- There are other technologies to remove rRNA and/or abundant transcripts from RNA-Seq libraries. One is NuGEN InDA-C technology that cleaves one of adapters from dscDNA before PCR amplification. They can design specific probes to any sequence to remove them from library.