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.

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Biomedical Research Support Shared Instrumentation Grants (S10)
Project #
1S10RR027052-01
Application #
7794425
Study Section
Special Emphasis Panel (ZRG1-GGG-A (30))
Program Officer
Birken, Steven
Project Start
2010-02-18
Project End
2011-08-17
Budget Start
2010-02-18
Budget End
2011-08-17
Support Year
1
Fiscal Year
2010
Total Cost
$489,250
Indirect Cost
Name
University of Massachusetts Medical School Worcester
Department
Genetics
Type
Schools of Medicine
DUNS #
603847393
City
Worcester
State
MA
Country
United States
Zip Code
01655
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