Hi, I am starting a project that will encompass the analysis of lncRNA (and eventually circRNA) from human cancer cell lines. I would like to analyze the differential expression of aforementioned RNA molecules, but also try to identify novel unannotated molecules, and find SNPs, InDels and splicing variants. What are the best companies to send RNA samples to in Europe? I already sent inquires to Genewiz and Novogene, but maybe you have your own favorite companies for RNA-seq projects?
Also, do you think 50M reads is sufficient for lncRNA project or I should go for 100M reads?
Thanks in advance for your suggestions and help!
Dear Michal,
sequencing companies nowadays are generally quite good, I think there are not too many go can go wrong with.
Regarding the depth, it depends on your aims. Do you want to find the large proportion of lnc/circRNAs or are you more interested in the obvious, well expressed ones? More reads is almost always better for the downstream analysis. It rather comes down to costs and if you are willing to pay double the price. If you have enough funding, go for 250 bp 100M reads, if you want to save some money go for something like 60-80M reads. In my experience, ~60M reads is a good minimum amount if you still want somewhat comprehensive results and you are not only looking at differential gene expression.
Hope this helps and with best regards,
Alexander
Dear Michal Wozniak
Send an email to the person below:
Yanara Marincevic-Zuniga, Ph.D. | Project coordinator, Researcher (SEQ)
SNP&SEQ Technology Platform | National Genomics Infrastructure (NGI)
Science for Life Laboratory | Uppsala University | Biomedical Center (BMC)
Husargatan 3 | Box 1432 | SE-751 44 Uppsala | Sweden
Phone: +46 (0)70 167 93 65
www.sequencing.se
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