Project description:Setaria viridis TPS1 was immunoprecipitated. The sample was separated by SDS-PAGE. The putative SvTPS1 band was sliced from the gel and analysed by mass spectrometry.
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:N6-methyladenosine (m6A) is a pivotal epitranscriptomic modification that regulates mRNA metabolism and plays critical roles in plant growth and environmental responses. However, the evolution and roles of m6A modifications in plant domestication remain largely unexplored. This study combined RNA-seq and MeRIP-seq data to compare m6A modifications profiles between foxtail millet (Setaria italica, Yugu1) and its wild ancestor S. viridis (A10). Peak calling analysis identified 6,928 m6A peaks associated with 6,407 protein-coding genes in Yugu1 and 6,274 m6A peaks in 5,858 genes in A10, respectively. Comparative analysis revealed numerous differentially expressed genes (DEGs) and differentially methylated peaks (DMPs), whose functions were elucidated by GO and KEGG enrichment analyses. Integration of DMPs paired with DEGs, we found 209 hyper-methylated peaks associated with upregulated transcription levels, and 90 hypo-methylated peaks associated with downregulated transcription levels. This dataset provides valuable resource for further investigating the roles of m⁶A modification in crop domestication.
Project description:A total of 18 libraries from Setaria viridis were constructed using the Illumina TruSeq sample preparation method. We used two biological replicate libraries from the leaf, whole panicles (inside leaf sheath), whole panicles (coming out of leaf sheath), whole panicles (completely out of leaf sheath), whole panicles (completely out of leaf sheath, after pollination), spikelet (inside leaf sheath), spikelet (coming out of leaf sheath), and spikelet (completely out of leaf sheath).