Abstract

The bioinformatics core will serve as a data clearinghouse, offering standardized quality assurance, sequence data handling and visualization to all four projects of this grant. By doing so it will ensure compatible and consistent data formats, parameter optimization and centralized storage. Existing UMMS bioinformatics pipelines will be optimized to provide and standardize read alignment, alignment processing (peak calling, transcript assembly, small RNA mapping, etc., enrichment analysis (Gene Ontology enrichments, etc.), and dataset integration (e.g. differential expression of piRNAs in different conditions). The centralized storage, processing and analysis of project data will thus significantly enhance integration between all four project components. Relevance The services provided by the Bioinformatics Core (Core C) are essential to research proposed by all four Projects. The core will provide storage, quality control, and preliminary analysis of high-throughput data from the three experimental projects (I-III), and make this data available to the computational project for in depth study (Project IV).

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD)
Type
Research Program Projects (P01)
Project #
5P01HD078253-03
Application #
9233747
Study Section
Special Emphasis Panel (ZHD1-DSR-L)
Project Start
2017-03-01
Project End
2020-02-29
Budget Start
2017-03-01
Budget End
2018-02-28
Support Year
3
Fiscal Year
2017
Total Cost
$72,224
Indirect Cost
$29,105

  Institution

Name
University of Massachusetts Medical School Worcester
Department
Biostatistics & Other Math Sci
Type
Domestic Higher Education
DUNS #
603847393
City
Worcester
State
MA
Country
United States
Zip Code
01655

  Publications

Dokshin, Gregoriy A; Ghanta, Krishna S; Piscopo, Katherine M et al. (2018) Robust Genome Editing with Short Single-Stranded and Long, Partially Single-Stranded DNA Donors in Caenorhabditis elegans. Genetics 210:781-787
Fu, Yu; Wu, Pei-Hsuan; Beane, Timothy et al. (2018) Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers. BMC Genomics 19:531
Seth, Meetu; Shirayama, Masaki; Tang, Wen et al. (2018) The Coding Regions of Germline mRNAs Confer Sensitivity to Argonaute Regulation in C. elegans. Cell Rep 22:2254-2264
Ishidate, Takao; Ozturk, Ahmet R; Durning, Daniel J et al. (2018) ZNFX-1 Functions within Perinuclear Nuage to Balance Epigenetic Signals. Mol Cell 70:639-649.e6
Zhang, Gen; Tu, Shikui; Yu, Tianxiong et al. (2018) Co-dependent Assembly of Drosophila piRNA Precursor Complexes and piRNA Cluster Heterochromatin. Cell Rep 24:3413-3422.e4
Shen, En-Zhi; Chen, Hao; Ozturk, Ahmet R et al. (2018) Identification of piRNA Binding Sites Reveals the Argonaute Regulatory Landscape of the C. elegans Germline. Cell 172:937-951.e18
Zhang, Donglei; Tu, Shikui; Stubna, Michael et al. (2018) The piRNA targeting rules and the resistance to piRNA silencing in endogenous genes. Science 359:587-592
Yu, Bowen; Lin, Yu An; Parhad, Swapnil S et al. (2018) Structural insights into Rhino-Deadlock complex for germline piRNA cluster specification. EMBO Rep 19:
Fu, Yu; Yang, Yujing; Zhang, Han et al. (2018) The genome of the Hi5 germ cell line from Trichoplusia ni, an agricultural pest and novel model for small RNA biology. Elife 7:
Gainetdinov, Ildar; Colpan, Cansu; Arif, Amena et al. (2018) A Single Mechanism of Biogenesis, Initiated and Directed by PIWI Proteins, Explains piRNA Production in Most Animals. Mol Cell 71:775-790.e5

Showing the most recent 10 out of 17 publications