Under the leadership of Dr. Alan Michelson and the steering committee (Drs. Mark Knepper, Warren Leonard and Keji Zhao), the DNA Sequencing Core has been successfully established to meet the increasing demands of intramural investigators for high-throughput sequencing, providing basic and advanced NGS services as well as development of novel NGS applications. (1) Consultation and data acquisition: In FY11, the DNA Sequencing Core has provided the state-of-the-art NGS services for DIR investigators in a cost effective and timely fashion. Diverse projects have been carried out including whole-genome sequencing, exome sequencing, DNA methylation sequencing, transcriptome sequencing (RNA-seq and small RNA sequencing), ChIP-seq and PAR-CLIP (genome-wide interaction map and nucleosome occupancy), reverse barcode sequencing (viral integration and ribozyme evolution), as well as innovative NGS applications (e.g. TSS-seq, PA-seq) to interrogate genome/transcriptome diversity. (2) In-depth data analysis: The DNA Sequencing Core has explored and implemented a wide range of open source and commercially available software packages for primary and secondary NGS data analysis. In addition, project-specific data analysis is further achieved by in-house software and algorithm development. As the result, it provides a large variety of tools for DIR investigators to convert the high-throughput data into biological meaningful findings for further examination. (3) Consultation and training: The DNA Sequencing Core has taken diverse venues to promote broad dissemination of NGS technology. Consultations are provided for experimental design and data analysis. The core also offers routine one-on-one training for library preparation and data analysis. (4) SOP development: Another key function of the DSC is SOP development. In collaboration with DIR investigators, high priority was set for technologies that are beneficial to multiple users or expected to facilitate the broad applications of high-throughput sequencing platform. We have developed and optimized protocol for (a) RNA-seq with limited starting materials and/or strand specificity;(b) mitochondria sequencing (C) genome-wide mapping transcriptional start sites and polyadenylation sites. In addition, we have been developing computational pipelines and workflow for systematic identification of SNPs, splicing variants and other regulatory events in gene expression network.
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