Bioinformatics Support for High Throughput Transcriptomics

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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.