Project description:This SuperSeries is composed of the following subset Series: GSE22360: Transcriptomic adaptations to symbiotic life in cnidarians : symbiotic vs bleached Anemonia viridis sea anemones GSE22361: Endoderm- vs ectoderm-specific expression of symbiosis genes in the snakelocks sea anemone Refer to individual Series
Project description:Setaria viridis, the wild ancestor of millet, exhibits strong repression of crown root growth in drought. We compare in gene expression in the S. viridis crown between drought vs watered treatments.
Project description:Parallel Analysis of RNA Ends (PARE) sequencing reads were generated to validate putative microRNAs and identify cleavage sites in Sorghum bicolor and Setaria viridis.
Project description:Analyses of new genomic, transcriptomic or proteomic data commonly result in trashing many unidentified data escaping the ‘canonical’ DNA-RNA-protein scheme. Testing systematic exchanges of nucleotides over long stretches produces inversed RNA pieces (here named “swinger” RNA) differing from their template DNA. These may explain some trashed data. Here analyses of genomic, transcriptomic and proteomic data of the pathogenic Tropheryma whipplei according to canonical genomic, transcriptomic and translational 'rules' resulted in trashing 58.9% of DNA, 37.7% RNA and about 85% of mass spectra (corresponding to peptides). In the trash, we found numerous DNA/RNA fragments compatible with “swinger” polymerization. Genomic sequences covered by «swinger» DNA and RNA are 3X more frequent than expected by chance and explained 12.4 and 20.8% of the rejected DNA and RNA sequences, respectively. As for peptides, several match with “swinger” RNAs, including some chimera, translated from both regular, and «swinger» transcripts, notably for ribosomal RNAs. Congruence of DNA, RNA and peptides resulting from the same swinging process suggest that systematic nucleotide exchanges increase coding potential, and may add to evolutionary diversification of bacterial populations.
Project description:Setaria viridis, the wild ancestor of millet, exhibits strong repression of crown root growth in drought. We compare in gene expression in the S. viridis crown between drought vs watered treatments. RNA from Lower region (crown) or Upper region (stem) of watered (W) or drought (D) treated Setaria plants were harvested at 6 or 9 days after sowing; there are 8 samples per biological repeat, 3 biological repeats.