CINCINNATI - Researchers at Cincinnati Children's Hospital Medical Center have developed a user-friendly, integrated platform for analyzing the transcriptomic and epigenomic "big data."
Reporting their platform in Genome Biology, scientists say that the new platform--called BioWardrobe--could help biomedical researchers answer questions about both basic biology and disease.
The recent proliferation of next-generation sequencing (NGS)-based methods for analysis of gene expression, chromatin structure and protein-DNA interactions have opened new horizons for molecular biology. These methods include RNA sequencing (RNA-Seq), chromatin immunoprecipitation sequencing (ChIP-Seq), DNase I sequencing (DNase-Seq), micrococcal nuclease sequencing (MNase-Seq), assay for transposase-accessible chromatin sequencing (ATAC-Seq) and others.
The sheer volume of the data obtained from sequencing requires computational data analysis. However, the bioinformatics and programming expertise required for this analysis is usually absent in typical biomedical laboratories, according to the authors. This results in data inaccessibility or delays in applying modern sequencing-based technologies to pressing questions in basic and health-related research.
"Although biologists can perform experiments and obtain the data, they often lack the programming expertise required to perform computational data analysis," says Artem Barski, PhD, senior author and assistant professor in the Divisions of Allergy and Immunology and Human Genetics at Cincinnati Children's. "BioWardrobe aims to empower researchers by bridging this gap between data and knowledge."
Andrey Kartashov, MS and Barski collaboratively developed BioWardrobe to facilitate the analysis and utilization of both newly generated and publically available datasets.
"Huge amounts of published data have been deposited in public databases, such as Gene Expression Omnibus or Short Read Archive, but remain inaccessible to majority of researchers due to lack of bioinformatics expertise," Kartashov said. "BioWardrobe allows biologists to analyze the data without having to learn how to program."
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More than twenty labs at Cincinnati Children's currently use BioWardrobe and research using the BioWardrobe platform has recently been published in several journals, including Developmental Cell and Mucosal Immunology.
Barski and Kartashov will continue improving BioWardrobe using an Innovative Core Facility grant provided by the University of Cincinnati's Center for Clinical and Translational Science and Training (CCTST). They also will continue using the platform in their own research on epigenetic regulation in the immune system, as well as in collaborative projects with other investigators.
The work to develop BioWardrobe was supported in part by the Cincinnati Children's Research Foundation, NHLBI NIH Career Transition Award (K22 HL098691 to Artem Barski) and the CCTST Innovative Core Facility grant (NIH/NCRR Institutional Clinical and Translational Science Award, 8UL1TR000077-06).
Related Links:
BioWardrobe Genome Biology Publication http://www.genomebiology.com/2015/16/1/158
BioWardrobe Website https://biowardrobe.com/
Barski Lab http://www.cincinnatichildrens.org/research/divisions/a/allergy-immunology/labs/barski/default/
Allergy and Immunology Research http://www.cincinnatichildrens.org/research/divisions/a/allergy-immunology/default/
Human Genetics Research http://www.cincinnatichildrens.org/research/divisions/h/genetics/default/
About Cincinnati Children's
Cincinnati Children's Hospital Medical Center ranks third in the nation among all Honor Roll hospitals in U.S.News and World Report's 2015 Best Children's Hospitals. It is also ranked in the top 10 for all 10 pediatric specialties, including a #1 ranking in pulmonology and #2 in cancer and in nephrology. Cincinnati Children's, a non-profit organization, is one of the top three recipients of pediatric research grants from the National Institutes of Health, and a research and teaching affiliate of the University of Cincinnati's College of Medicine. The medical center is internationally recognized for improving child health and transforming delivery of care through fully integrated, globally recognized research, education and innovation. Additional information can be found at http://www.cincinnatichildrens.org. Connect on the Cincinnati Children's blog, via Facebook and on Twitter.
Journal
Genome Biology