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Old 05-14-2013, 07:35 AM   #5
Eric Fournier
Location: Quebec, Canada

Join Date: Jul 2011
Posts: 21

Hello Dan,

we ran our samples on five different lanes. Each lane used 6 of 8 possible multiplex tags from the Encore multiplex kit (which uses 4nt tags). This actually caused a small problem, since one of the combination of 6 tags that we used caused library complexity for the first four nucleotides to go down substantially, which was reflected as low quality values across the whole library.

The ERCC spikes were added immediatly after RNA extraction, while the multiplexing was done just prior to sending the libraries to the sequencing center.

Since we had 10 different tissues and that we were not interested in any particular pairwise comparison, we did not use th Exfold mix to assess fold-change effects. Rather, we used only mix 1 from the ERCC to have one shared standard across all libraries.
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