ChIP-seq on Drosophila embryos using Illumina

[janews]

Hi,

I am going to do ChIP-seq experiment on Drosophila embryos and to keep the expenses as low as possible, I am going to run multiple barcoded samples on the same lane. The service I am going to use allows us to run as many as 12 samples on the same lane. Actually, I am IPing some TFs from staged embryos, and I am not sure how many samples I could run in parallel on the same lane without compromising the coverage. Does anybody know the answer to this question?

Thanks

[mudshark]

Hi,
that will very much depend on

a) how many reads you get in total
b) how evenly the reads are distributed among the samples
c) how well your IP works
d) how your target proteins are distributed, how many binding sites they have
e) how sensitive you want to be

in Drosophila you might need at least >3x10^6 MAPPED reads per sample to get a decent coverage. consequently you might need >6x10^6 reads per sample. to be on the safe side I would not multiplex more than 8 samples if average runs on your sequencer provide 50x10^6 reads in total.


of course that is just a rough guess