Are ribosomal protein coding genes depleted as well during rRNA depletion?
0
0
Entering edit mode
6 months ago
akibio • 0

Hi all,

I'm pretty confused as to which RNA molecules are depleted during rRNA depletion. Part of my confusion comes from my colleagues questioning me. In my analysis, I aligned RNA-seq reads to a reference fasta which contains all coding sequences for the organism that the reads were collected from. The reference contains many coding sequences which are ribosomal protein coding genes. My understanding is that we want these in the reference. Some colleagues disagree and the literature on this subject is non-existent as far as I can tell. So, do we expect these ribosomal protein coding genes to be in the sample after rRNA depletion, meaning that we definitely want them in our alignment reference? Happy to elaborate further if necessary.

Thanks!

rRNA RNA-seq depletion annotations • 335 views
ADD COMMENT
0
Entering edit mode
6 months ago
GenoMax 107k

From NEBNext rRNA depletion kit manual:

The NEBNextrRNA Depletion Kit (Human/Mouse/Rat) depletes both cytoplasmic (5S rRNA, 5.8SrRNA, 18S rRNA and 28S rRNA) and mitochodrial ribosomal RNA (12SrRNA and 16S rRNA) from human, mouse and rat total RNA preparations.

From ThermoFisher

Ribosomal removal methods address these issues by directly depleting the rRNA while leaving other transcripts intact.


Ribosomal proteins are expressed in various tissues (GTeX RNAseq method is described here and use oligo-dT bead selection). Some examples below.

https://www.gtexportal.org/home/gene/RPS2
https://www.gtexportal.org/home/gene/RPL6
https://www.gtexportal.org/home/gene/RPL4 (Mitochondrial)

ADD COMMENT

Login before adding your answer.

Traffic: 2248 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6