Project description:To gain insights into the molecular mechanisms controlling bamboo growth, mRNA differential display was used to clone genes that are differentially expressed in various tissues of shoots at different growth stages, and their expression patterns were further validated by cDNA microarray. A number of genes and signaling pathways are proposed to have significant roles in controlling the elongation of the bamboo culm. Etiolated shoots (average height: 15 cm) that had not yet emerged from the ground and green shoots (average height: 100 cm) of Bambusa oldhamii were collected. The shoots were divided into three parts, the culm base, the middle and the top regions for RNA extraction and processing. The RNA from the middle region of the etiolated shoots was used as a reference in microarray comparisons.
Project description:DNA-prep of Col and hcr2 mutant from seedling and bud sample. DNA was extracted using DNeasy Plant Mini Kit (Qiagen 69104, USA). Library construction and bisulfite conversion was performed using EZ DNA Methylation-Gold kit (ZYMO). DNA libraries are sequenced on the DNBseq platform (BGI, Hong Cong).
Project description:We benchmark Illumina’s HiseqX10 instrument against Beijing Genomics Institute’s (BGI) DNBSEQ-G400 platform, a considerably cheaper sequencing alternative. For comparisons, the same bulk ATAC-seq libraries generated from pluripotent stem cells (PSCs) and fibroblasts were sequenced on both platforms. Both instruments generate sequencing reads with comparable mapping rates and genomic context. However DNBSEQ-G400 data contained a significantly higher number of small, sub-nucleosomal reads (>30% increase) and a reduced number of bi-nucleosomal reads (>75% decrease), which resulted in narrower peak-bases and improved peak calling, enabling the identification of 4% more differentially accessible regions between PSCs and fibroblasts. Ability to identify master TFs that underpin the PSC state relative to fibroblasts, including aggregate and de novo foot-printing capacity, were highly similar between data generated on both platforms.
