tsoumakidou[at]fleming.gr

Dear Dr Tsoumakidou,

the analysis of your RNAseq experiment has finished.
The samples and the number of reads obtained are:
GK3R112-Empty2 3657161
GK3R113-Empty3 3650945
GK3R114-Empty4 4109139
GK3R116-Wnt2 3533012
GK3R117-Wnt3 3549158
GK3R118-Wnt4 3946422


At 
http://genomics-lab.fleming.gr/cgi-bin/hgTracks?db=mm10&hubUrl=http://genomics-lab.fleming.gr/fleming/GKlab/run356/hub.txt
you will find tracks for all samples integrated in our UCSC genome browser mirror.
These tracks are sampled to smallest library (GK3R116-Wnt2 with 3533012 reads).

At
http://genomics-lab.fleming.gr/fleming/GKlab/run356/metaseqr_quantseq_run356
you will find the metaseqR [1] differential gene expression analysis using
the contrast
Empty_vs_Wnt, which is
(note the used naming convention: in A_vs_B, A is always the reference!).

As I noted unusual clustering for the sample GK3R114-Empty4 in the MDS plot,
I repeated the analysis without this sample. The results at
http://genomics-lab.fleming.gr/fleming/GKlab/run356/metaseqr_quantseq_run356_woE4
have twice the number of sig. diff. exp. genes.

With best regards,
Martin

[1] Moulos P and Hatzis P “Systematic integration of RNA-Seq statistical
algorithms for accurate detection of differential gene expression
patterns.” Nucl. Acids Res. (2014)
doi: 10.1093/nar/gku1273
http://nar.oxfordjournals.org/content/early/2014/12/01/nar.gku1273.abstract.