This application requests funding for an Illumina (Solexa) Genome Analyzer IIx massively parallel sequencer to enhance the capacity and capabilities of the Deep Sequencing Core Laboratory at UMass Medical School. Using a first generation Solexa instrument available in the core facility a number of laboratories have developed methods for mapping functional genomic elements and genomic architecture, identifying populations of small ncRNAs present in various species and cell types, and determining DNA-binding specificities for entire families of DNA-binding domains. The demand for this sequencing service is outstripping the present capacity of our core facility;the number of new users is growing rapidly with NIH-funded projects in areas of human disease such as ALS, Schizophrenia, Diabetes, Cancer and Cardiovascular disease. Addition of another deep sequencing instrument with improved capacity and capabilities is critical to meet the needs of these NIH-funded investigators. Twenty-four NIH funded projects that will directly benefit from this new capacity are described within our application.
|Hainer, Sarah J; McCannell, Kurtis N; Yu, Jun et al. (2016) DNA methylation directs genomic localization of Mbd2 and Mbd3 in embryonic stem cells. Elife 5:|
|Chen, Poshen B; Chen, Hsiuyi V; Acharya, Diwash et al. (2015) R loops regulate promoter-proximal chromatin architecture and cellular differentiation. Nat Struct Mol Biol 22:999-1007|
|Hainer, Sarah J; Gu, Weifeng; Carone, Benjamin R et al. (2015) Suppression of pervasive noncoding transcription in embryonic stem cells by esBAF. Genes Dev 29:362-78|
|Hainer, Sarah J; Fazzio, Thomas G (2015) Regulation of Nucleosome Architecture and Factor Binding Revealed by Nuclease Footprinting of the ESC Genome. Cell Rep 13:61-69|
|Tsai, Hsin-Yue; Chen, Chun-Chieh G; Conte Jr, Darryl et al. (2015) A ribonuclease coordinates siRNA amplification and mRNA cleavage during RNAi. Cell 160:407-19|
|Chen, Poshen B; Zhu, Lihua J; Hainer, Sarah J et al. (2014) Unbiased chromatin accessibility profiling by RED-seq uncovers unique features of nucleosome variants in vivo. BMC Genomics 15:1104|
|Moroz, Leonid L; Kocot, Kevin M; Citarella, Mathew R et al. (2014) The ctenophore genome and the evolutionary origins of neural systems. Nature 510:109-14|