Newbie Question on sample size

[adnancho]

Hi I'm trying to bring RNA-seq into our lab. Our samples will be variable +/-1000 cells, 3-4000 cells total. After I lyse the cells for RNA, should I run the entire sample or should I get the concentration of RNA and use a specific total RNA amount for making each library? How do you adjust for between sample variability and for that matter within sample variability? Or does this come out in the wash during normalization of the data?

Thank you.

[nucacidhunter]

Amount of RNA for library prep would be based on recommendations by the kit manufacturer and varies from kit to kit.

[AllSeq]

That level of variability will 'come out in the wash' long before you get to generating data. Even if you start with variable amounts of input RNA, you'll aim for putting equivalent amounts of library DNA onto the flow cell. As long as you have enough input RNA for the kit, you should be ok. That said, kits often will produce different results with different starting amounts - you'll start seeing noisier data as you push towards the lower limits of what the kit can handle.