Jose M Perez's List: Research papers

• Spontaneous epigenetic variation in the Arabidopsis thaliana methylome
• spontaneous DNA mutation rates
• one single-base-pair mutation per haploid genome and generation
• whole-genome cytosine methylation
• Illumina sequencing
• nuclei extraction buffer
• Genomic DNA was extracted using the Qiagen Plant DNeasy kit (Qiagen)
• Trizol (Invitrogen) method
• Total RNA
• Residual DNA was eliminated by DNase I
• Preparation of DNA libraries for bisulphite sequencing was adapted from ref. 14
• SHORE pipeline
• to trim and quality-filter the reads
• mapping tool GenomeMapper
• aligned using BWA
• pairwise comparisons of expression were performed using the DEseq package

14 more annotations...

• deletion or rearrangement with consequent phenotypic effects
• segmental duplications cover 5.3% of the  euchromatic genome
• extreme case is chromosome Y
• carries segmental duplication along >25%
• total number of protein-coding genes is in the range 20,000–25,000
• clusters of nearby homologous genes
• indicative of local gene duplication
• recent duplications
• enriched in genes with immune
• and olfactory function
• reproductive functions

9 more annotations...