How many cells need to be seeded for RNA-seq analysis

Question

[sacha.bohler]

Hello everybody,

I am planning a large scale RNA-seq experiment on SH-SY5Y cells, and was wondering how many cells I need to have per sample to extract a sufficient amount of RNA.

Many thanks in advance,

Sacha

Answer 1

[jotan]

The best thing to do is to ask your sequencing facility.

For a bog-standard PolyA selected RNA-Seq, you want around 1-3 ug of total RNA. However, some facilities have the capacity to go much lower than this (100 ng) if you need to.

The number of cells needed will depend on the cell type but 1-2 e5 is probably plenty if you're aiming for the lower limit (1 ug). If your cells are easy to grow then seed more and extract more RNA and then just give the sequencing facility as much as they need.