Bioinformatics Support for High Throughput Transcriptomics

本次工作的主要成果包括：1）TempO-Seq QC和数据分析管道的增强和部署。Sciome部署了许多增强功能，以详细说明用于分析TempO-seq数据（HTT数据的代表性平台）的数据质量控制工作流程。 增强功能包括通过各种可视化和分析方法进行样本检测。HTT数据的QA/QC数据报告平均不到5个工作日。 2)Sciome在NIEHS计算机基础设施内对高通量转录组学数据进行存档和管理。这些活动包括详细的生物信息学支持，以检索，组织，QC和存档DNTP在各种HTT项目中收到的原始TempO-Seq数据。 NIEHS科学IT，其他DNTP科学家和其他承包商参与了开发这一成就。3)Sciome进行了HTT项目#Tgmx15 TempO-Seq研究的分析，对涉及肝脏和肾脏的20种化学物质进行了详细分析，包括肝脏和肾脏中所有20种化学物质的测序QC、离群值检测、归一化、外推、DEG/DEP分析、网络分析和BMDExpress剂量反应分析。 Sciome使用了一种新的网络分析方法来确定Tgmx 15研究中彼此相似的化学物质;并将它们与公共签名数据进行比较，以预测作用模式。 这些数据正在以同行审查的手册形式编写。

Major accomplishments of this task include: 1) Enhancement and deployment of TempO-Seq QC and data analysis pipeline. Sciome deployed a number of enhancements to detail a data quality control workflow for analysis of TempO-seq data (representative platform for HTT data). Enhancements included sample detection via various visualization and analysis approaches. the QA/QC data reports for HTT data averaged less than five business days. 2) Archival and management of high throughput transcriptomics data within the NIEHS computer infrastructure was performed by Sciome. These activities included detailed bioinformatics support to retrieve, organize, QC and archive original TempO-Seq data received by DNTP across various HTT projects. NIEHS Scientific IT, and other DNTP scientists and other contractors were involved in developing this accomplshment. 3) Analysis of HTT project #Tgmx15 TempO-Seq study was conducted by Sciome for a detailed analysis of 20 chemicals involving liver and kidney TempO-Seq dataset including sequencing QC, outlier detection, normalization, extrapolation, DEG/DEP analysis, network analysis and BMDExpress dose response analysis for all 20 chemicals in liver and kidney. Sciome used a novel network analysis method to determine chemicals within the Tgmx15 study that are similar to each other; and also compared them with public signature data to predict modes of action. These data are being prepared in peer-reviewed manuscirpt form.