Science News
from research organizations

Furthering data analysis of next-generation sequencing to facilitate research

Date:
August 11, 2015
Source:
Cincinnati Children's Hospital Medical Center
Summary:
A user-friendly, integrated platform for analyzing the transcriptomic and epigenomic 'big data' has been developed by researchers. The scientists say that the new platform -- called BioWardrobe -- could help biomedical researchers answer questions about both basic biology and disease.
Share:
FULL STORY

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."


Story Source:

Materials provided by Cincinnati Children's Hospital Medical Center. Note: Content may be edited for style and length.


Journal Reference:

  1. Andrey V. Kartashov, Artem Barski. BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data. Genome Biology, 2015; 16 (1) DOI: 10.1186/s13059-015-0720-3

Cite This Page:

Cincinnati Children's Hospital Medical Center. "Furthering data analysis of next-generation sequencing to facilitate research." ScienceDaily. ScienceDaily, 11 August 2015. <www.sciencedaily.com/releases/2015/08/150811132544.htm>.
Cincinnati Children's Hospital Medical Center. (2015, August 11). Furthering data analysis of next-generation sequencing to facilitate research. ScienceDaily. Retrieved May 29, 2017 from www.sciencedaily.com/releases/2015/08/150811132544.htm
Cincinnati Children's Hospital Medical Center. "Furthering data analysis of next-generation sequencing to facilitate research." ScienceDaily. www.sciencedaily.com/releases/2015/08/150811132544.htm (accessed May 29, 2017).

RELATED STORIES