Data collection for the epigenetics and chromatin (EpiC) research laboratory

DNA is packaged into chromatin which is differentially modified to reflect gene expression. The rapid advances in DNA sequencing technology in recent years has led to the generation of massively detailed datasets which are available online (http://www.nature.com/encode/#/threads). The ability to freely analyse these datasets (histone modifications, DNA methylation, DNAseI hypersensitive sites, transcription factor binding sites, nucleosome positioning, RNA expression data) is crucial for any lab studying epigenetics and chromatin.

The EpiC lab (http://www.med.monash.edu.au/biochem/staff/wong.html) is attempting to understand the role of a histone variant, H3.3, at specialised regions of the genome. In order to achieve this, access, storage and analysis of large genome-wide sequencing files is required as well as cross-reference publicly available datasets to any data generated within the lab.

The main analysis software is SeqMonk. This software can only be used via a graphical user interface and will require access to large data sets, and will generate data sets of the order of 4TB. Eventually specific data sets will need to become accessible to groups outside Monash University, particularly to enable visualisation via the UCSC Genomic Browser @ https://genome.ucsc.edu/.

DNA被包装为染色质（Chromatin），染色质会发生差异化修饰以反映基因的表达状态。近年来DNA测序技术的飞速发展催生了海量精细的数据集，相关数据可在线获取（http://www.nature.com/encode/#/threads）。自由分析这类数据集（包括组蛋白修饰、DNA甲基化、DNA酶I（DNAseI）超敏位点、转录因子结合位点、核小体定位以及RNA表达数据）的能力，对于所有研究表观遗传学（Epigenetics）与染色质的实验室而言至关重要。

EpiC实验室（http://www.med.monash.edu.au/biochem/staff/wong.html）正致力于解析组蛋白变体H3.3在基因组特定位点的功能。为达成这一研究目标，该团队需要获取、存储并分析全基因组范围的大型测序文件，同时还需将实验室内部生成的数据与公开数据集进行交叉比对。

核心分析软件为SeqMonk。该软件仅能通过图形用户界面（Graphical User Interface，GUI）使用，且需要处理大型数据集，同时会生成约4TB量级的数据集。最终，部分特定数据集需要向莫纳什大学以外的研究团队开放，尤其是为了支持通过UCSC基因组浏览器（UCSC Genomic Browser，https://genome.ucsc.edu/）进行可视化展示。