Project description:Performances of flax gene expression analyses were compared in two categories of Nimblegen microarrays (short 25-mers oligonucleotides and long 60-mers oligonucleotides) Results obtained in this study are described in Intra-platform comparison of flax (Linum usitatissimum L.) high-density Nimblegen DNA microarrays submitted to Journal of Computational Biology
Project description:Whole-genome bisulfite sequencing (WGBS) was employed for identification of differential DNA methylation profiles among control and heat-stressed seedlings of a fibre flax (Linum usitatissimum L.) var., JRF-2. It was identified as a tolerant variety of heat stress-induced oxidative damage. High-quality genomic DNA from four samples comprised 3-week-old control and heat-stressed (40±2°C) seedlings, with or without treated with 5-Azacytidine (hypomethylating agent). High-quality and filtered paired-end Illumina reads were aligned to the flax reference genome, assembled in chromosomes, using bwa-meth tool, followed by methylation loci (5-mC) calling using the MethylDackel software. Differentially methylated regions (DMRs) between the control and other samples were identified using the methylKit and annotated using genomation package for their precedence in the promoter/exon/intron/intergenic regions. The DMRs comprised both hyper- and hypomethylated loci, but the latter found dominated due to heat stress in flax seedlings. The WGBS in flax for heat stress will provide a platform to identify epigenetic loci responsible for heat-stress adaptation in flax.
Project description:Performances of flax gene expression analyses were compared in two categories of Nimblegen microarrays (short 25-mers oligonucleotides and long 60-mers oligonucleotides) Results obtained in this study are described in Intra-platform comparison of flax (Linum usitatissimum L.) high-density Nimblegen DNA microarrays submitted to Journal of Computational Biology We compared two categories of flax target probes: short (25-mers) oligonucleotides and long (60-mers) oligonucleotides in identical conditions of target production, design, labelling, hybridization, image analyses, and data filtering. This comparison was realized with two different flax samples and each RNA sample was used for the two categories of arrays. Experiments were realized in order to discriminate specific gene expression profiles of two different flax tissues (outer and inner stem tissues).
Project description:Three 2cm segments were excised from different parts (TOP, MID, BOT) along the vertical axis of a 4 week old (25cm) stem of flax (L. usitatissimum) were compared using a cDNA amplicon array. Each segment represented a different developmental stage, especially in relation to bast fibre differentiation (i.e. TOP= elongation, MID=transition, BOT= thickening). Only the cDNAs that showed the highest differential expression were sequenced.
