Inexpensive RNA-Seq Kit with OK Results

August 06, 2018

UCSF
Urology
Grad Student

Overall

Quality of Results

Ease-of-Optimization

What do these ratings mean?
Write a Review

Company:

Lexogen

Product Name:

QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina

Catalog Number:

015.96.

I was trying to see how the loss of an RNA-binding protein changes translation and gene expression in mouse embryonic stem cells. I was looking for an inexpensive RNA-Seq kit to try. This kit is one of the cheapest, but some samples sometimes end up with lots of rRNA contamination.

Experimental Design and Results Summary

Application

RNA-Seq

Starting Material

Mouse RNA

Protocol Overview

Followed the kit protocol. Put in RNA, perform oligo-dT cDNA synthesis, add adapters, PCR, purify, then sequence.

Tips

Be careful to not let the reaction cool during the oligo-dT cDNA synthesis or you will get mispriming from the oligo-dT primer

Results Summary

The results from this kit are just ok. Some samples have high levels of rRNA contamination resulting in a lower percentage of reads mapping to coding RNA. However, differentially expressed genes mostly match results from full length RNA-seq kits.

DOI or PMID #

N/A

Additional Notes

N/A

Image Gallery

Summary

The Good

Cheap

The Bad

Sometimes high levels of rRNA contamination in samples, not very responsive support.

The Bottom Line

This kit is one of the cheapest ways to do RNA-SEq, but be prepared for some rRNA contamination and to sequence deeper than expected. Also, note that since this is only 3' counting, you will not get information about differential splicing.

Join the discussion