Dear Fani,

the analysis of your QUANTseq experiment has finished.
The samples and the number of reads obtained are:
sample           n_reads        
GK3R188-Wt1      1841923 
GK3R189-Wt2      5287804 
GK3R190-C1       5022295 
GK3R191-C2       5098218 
GK3R192-C3       6231647 
GK3R193-Tg197-1  6337949 
GK3R194-Tg197-2  6923642 
GK3R195-Tg197-3  7029048 
GK3R196-Tg197-C1 6158257 
GK3R197-Tg197-C2 1642910 
GK3R198-Tg197-C3 4487739 


At
http://genomics-lab.fleming.gr/fleming/GKlab/run403/metaseqr_GKlab_run403/
you will find the metaseqR [1] differential gene expression analysis using
the contrasts
LiveInv_vs_FIXED, which is
(note the used naming convention: in A_vs_B, A is always the reference).
In the "Results" section, there are links to download the diff. expr. results
under "DEG table", "Download the whole result list".

Based on the MDS plot and the smaller number of reads, I'd recommend a reanalysis with
GK3R197-Tg197-C2
omitted.

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.