Illumina HiSeq 2000 paired end sequencing; Analysis of the bread wheat grain transcriptome reveals complex genome interplay in a hexaploid cereal.
Analysis of the bread wheat grain transcriptome reveals complex genome interplay in a hexaploid cereal.
Bread wheat cv Chinese Spring plants were grown in phytotrone chambers with cycles of 16 h of light at 20C and darkness of 8h at 15C.  Each room held 75 pots with three plants each. Plants were tagged at anthesis and the middle part of ears were harvested at 10, 20 and 30 DPA and stored at -80C. Seeds were dissected using dry ice and covered by RNAlater-ICE (Life Technologies, NY, USA) under the dissecting microscope. Embryos were removed and grains cut in slices for isolation of the aleuron layer, transfer cells and starchy endosperm. Dissected tissues were frozen in liquid nitrogen and stored at -80C for subsequent RNA isolation. Tissues from 15 pots per room were pooled before RNA isolation. Two replicate samples were made per room, giving a total of four replicates per tissue and time points. Total RNA was extracted from frozen plant material using the RNeasy Lipid Tissue Mini kit (QIAGEN, Hilden, Germany; http://www.qiagen.com/applications/plant). Illumina TruSeq RNA Sample Preparation Kits v2
Experimental Factor: block
room1
Experimental Factor: developmental stage
10 days post anthesis
Experimental Factor: organism part
whole endosperm