Martin Reczko Thu, Jun 29, 2017 at 4:28 PM To: Panagiota Kafasla , Kontoyiannis Dear Yiota and Dimitris, attached is the list of alternative spliced (AS) genes in the overall RNAseq wt vs ko comparison. As the requirement to have the same alternative form in all conditions is too strict, I tested for alternative splicing in each condition and report the condition where AS occurs in the column maxAnticorrCond. These 19 genes thus have significant differential expression for 2 isoforms in the overall wt vs ko comparison and the expression of these 2 isoforms is anticorrelated (<= -0.5) in at least one condition. BW, Martin [Quoted text hidden] transcripts_wt_vs_ko_alt_spliced_in_at_least_one_condition.xlsx 16K ASwell #Alternative Splicing With stringtie Expressions anticoreLation maximized Alternative Splicing With EdgeR differentiaL expression anticorreLation based on StringTie Dear Yiota, please see attached the alternative splicing analysis for each condition and isoform expression plots for the top alternative spliced gene. I will explain details later. BW, Martin #@ Mon, Jun 19, 2017 at 11:36 AM To: Panagiota Kafasla Dear Yiota, please see attached the alternative splicing analysis for each condition and isoform expression plots for the top alternative spliced gene. I will explain details later. BW, Martin [Quoted text hidden] 10 attachments EdgeR top1-0h-Isoform expression in Zfp143.png 139K EdgeR top1-2h-Isoform expression in Kif5c.png 91K EdgeR top1-6h-Isoform expression in Katna1.png 112K EdgeR top1-IFN-Isoform expression in Gm12250.png 126K EdgeR top1-IL4-Isoform expression in Dyrk2.png 84K edgeRtranscriptsExpr-0h.withGID.csv.alt_spliced.xlsx 14K edgeRtranscriptsExpr-2h.withGID.csv.alt_spliced.xlsx #@ Martin Reczko Wed, Jun 14, 2017 at 8:38 PM To: Panagiota Kafasla Re: what the samples are Dear Yiota, attached are my findings concerning alternative splicing in the RNAseq data. Comparing all wt vs all ko samples, I get 23 differentially expressed transcripts (q-value <=0.05). Using the criterium for alternative splicing, that a different transcript of the same gene should also be differentially expressed (p-value < 0.05), 14 genes are alternatively spliced (see attached xls). I've generated transcript visualizations for those 14 (attached). The polysome seq tracks are at: http://genomics-lab.fleming.gr/cgi-bin/hgTracks?db=mm9&hubUrl=http://genomics-lab.fleming.gr/fleming/DKlab/mr/ Polysomes/www/Phub.txt These are generated by merging replicates and sampling to the smallest library pair (WT_IL4 containing 9826554 reads). The libraries without replicates are not sampled. BW, Martin Isoform expression in Atpaf2.png 131K Isoform expression in Cast.png 169K Isoform expression in Csde1.png 111K Isoform expression in Dctn2.png 101K