Brachypodium distachyon Transcriptome or Gene expression

Deep sequencing of Brachypodium distachyon small RNA from panicles (flowers) was done to analyze the genome-wide distribution patterns of 1) total small RNA reads and loci, 2) 21 and 24 nucleotide repeat-normalized reads and 3) 21 and 24 nucleotide phased siRNA clusters relative to gene and transposable element density. Overall design: Small RNA were extracted from total RNA by size fractionation and converted to DNA amplicons by serial adaptor ligation to both ends followed by RT-PCR. DNA amplicons were sequenced using an Ilumina Genome Analyzer. Resulting sequences were computationally trimmed to remove 3' adaptor sequences. Raw data for GSM506621 was not provided.

本研究对取自穗部（花器官）的二穗短柄草（Brachypodium distachyon）小分子RNA（small RNA）开展深度测序，旨在分析三类对象的全基因组分布模式：1）总小分子RNA测序读段（reads）及基因座（loci）；2）经重复序列归一化处理的21与24核苷酸长度测序读段；3）结合基因与转座元件（transposable element）密度的21、24核苷酸相位型小干扰RNA（phased siRNA）簇。总体实验设计：通过尺寸分级分离从总RNA中提取小分子RNA，随后在其两端依次连接接头以制备DNA扩增子，再经逆转录聚合酶链式反应（RT-PCR）进行扩增；所得DNA扩增子采用Illumina基因组分析仪完成测序。后续通过计算处理对所得测序序列进行修剪，以移除3'端接头序列。未提供GSM506621的原始数据。