1. Tom Brutnell Pinghua Li Lin Wang C4 photosynthesis – visualization of RNA seq datasets

2. Ligule leaf 3 Ligule leaf 2 0 to +1 from base base 4 tip -1 to 0 from lf. 2 ligule +4 +5 from lf. 2 ligule -2 to -1 from tip cm B C D E A Leaf 2 ligule Leaf 3 tip

4. XML

5. The Wilcoxon test tests the hypothesis that objects within one functional class behave different from the rest of the objects. For simplicity you can think of the Wilcox test as a rank based t-test. Pageman in analyzing pathways from four sections and LCM Wilcoxon test was used for statistics Target: figure out the pathways that significantly changed in differentiation and development

6. Bin (category) structure 1.PS 1.1 PS. Light reaction 1.1.1 PS. Light reaction: PSII Left 3 columns are four sections log 2 fold change (all compared with base) Blue-up; Red-down Right 2 columns are LCM Blue-BS; Red-ME

7. 1.5

8. 1.PS C4 pathways (light reaction-cyclic e flow + calvin cycle + carbon transporters + maybe photorespiration) 2.Sugars Sucrose/Starch/TPSTPP/raffinose/myo-inositol? 3.Cell wall Precursor/ cellulose/ cell wall protein 4. Lipid- FA synthesis and enlongation 5.Hormone BR/GA/JA/Aux and ET? 6.Redox thioredoxin/ascobate/glutathione/glutaredoxin 7.TF C2C2 (Zn) Dof/C2C2(Zn) Co-like/G2-like/MYB/TCP/WRKY/bZip (LCM only) 8.Histone/DNA methytransferase 9.Signalling Receptor kinase (leucin-rich III, IV, VII and VIII, XI)/wall associated kinase/G protein/MAPK3) 10. Transporters C4 carbon/sulphate/AA/vesicles