#@ 20032019 Hi Martin, I learnt that the latest RNAseq that we did is being analysed. I would like to ask you to also include in the analysis run296. More specifically we would like the following comparisons: COLVI_AOM DSS GFP vs COLVI_AOM DSS TOM COLVI_AOM DSS GFP vs COLVI_AOM DSS unsort COLVI_AOM DSS TOM vs COLVI_AOM DSS unsort COLVI_AOM DSS GFP vs G (run296) COLVI_AOM DSS TOM vs T (run296) COLVI_AOM DSS unsort vs U (run296) Let me know if you need more information. Thank you! Vasso #@ with GIH2: https://genomics-lab.fleming.gr/fleming//GKlab/Kolliaraki/run340_run387/metaseqr_quantseq_run340_run387b => GIH_vs_GFP: 800 (15) statistically significant genes of which 529 (15) up regulated with GIH2 and GK3R137r-UNS-DARE1-TEST1 GK3R138r-UNS-DARE2-TEST2 GKlab: (re-)analysis of run386,387 Vasiliki Koliaraki Thu, May 31, 2018 at 2:16 PM To: Martin Reczko Dear Martin, thank you very much for your quick response! I was also looking again at the analysis of run387 with run340. I would like to ask you to include also sample GIH2 for the GFPvsGIH comparison, as I think that we are loosing many important deregulated genes by keeping only the two samples and at least for the genes that I have searched for it looks fine, so there is probably no reason for omitting it. I have seen that the same stands also for the UNSvsUI comparison. Many genes that have a big and seemingly consistent difference are not in the end statistically significant. For example there is a very big list of genes with no expression in the UNS samples and similar number of counts in the UI2-3 samples that does not come out as statistically significant. However, the UI1 sample is really bad, so I guess that we cannot do anything in this case, right? Thanks a lot! Vasso Vasiliki Koliaraki, PhD BSRC "Al. Fleming" 34 Fleming Street 16672, Vari, Greece Tel: +30-210-9656310 (ext. 206) # Dear Martin, I am looking now in more detail at the data from runs 386 and 394 and I would like to ask you if you could also to do the following extra 2 comparisons: ML vs CU CL vs MU Thank you very much! Vasso #@ run340,386,387 r386 Ion 386 GK3R140-MU1 25 5.1 GK3R141-MU2 26 3.7 GK3R142-MU3 27 5.3 GK3R143-MI1 28 4.6 GK3R144-MI2 29 4.4 GK3R145-MI3 30 3.8 GK3R146-CU1 31 5.3 GK3R147-CU2 32 4.7 GK3R148-CU3 33 3.7 GK3R149-CI1 34 1.5 GK3R150-CI2 35 2.4 Ion 387 GK3R131r-GFP-DARE1 25 4.9 GK3R132r-GFP-DARE2 26 4.2 GK3R133r-GFP-DARE3 27 4.0 GK3R134r-TOM-DARE1 28 5.9 GK3R135r-TOM-DARE2 29 3.4 GK3R136r-TOM-DARE3 30 6.0 GK3R137r-UNS-DARE1 31 4.9 GK3R138r-UNS-DARE2 32 4.5 GK3R139r-UNS-DARE3 33 2.9 r388: GKlab_APardo-12-3RNAseq_VKol-1reseq GK3R149-CI1 34 1.1 Combine with same sample @ ion 386 V. Koliaraki r389: GKlab-GK3R151r-163_ITlab-ITC278-281_PHlab-PH4C2 GK3R151r-CI3 36 0.4 To replace same sample @ ion 386 V. Koliaraki r391 IonXpress_036 GK3R151r-CI3 IonXpress_039 GK3R163-ColVICreLtbR-L12 GKlab: (re-)analysis of run386,387 Vasiliki Koliaraki Tue, Mar 13, 2018 at 2:38 PM To: Pantelis Hatzis , Martin Reczko Dear Both, I had a very quick look at run387 and it looks good! This is great as it was from only 50.000 cells per sample. Before I continue with the analysis I would like if possible to compare it also to run340, specifically the following: UNS vs UI (omit UI1) GFP vs GIH TOM vs TI Thank you very much! Vasso Vasiliki Koliaraki, PhD BSRC "Al. Fleming" 34 Fleming Street 16672, Vari, Greece Tel: +30-210-9656310 (ext. 206) GKlab: (re-)analysis of run386,387 Vasiliki Koliaraki Fri, Apr 20, 2018 at 4:25 PM To: Martin Reczko Cc: Pantelis Hatzis , Harokopos Vaggelis Dear Martin, I would like the following analysis for these last 6 samples combined with run386: ML vs MU CL vs CU ML vs CL MI vs CI ML vs MI CL vs CI MU vs CU Also, I would like to remind you of the re-analysis of run387 with run340 and specifically the following additional comparisons: UNS vs UI (omit UI1) GFP vs GIH TOM vs TI Thanks a lot, Vasso