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BMC Res Notes. 2015 Apr 3;8:124. doi: 10.1186/s13104-015-1089-9.

An automated method for efficient, accurate and reproducible construction of RNA-seq libraries.

Author information

1
Department of Biochemistry and Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, 701 Ellicott St., 14203, Buffalo, NY, USA. tsompana@buffalo.edu.
2
Department of Biochemistry and Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, 701 Ellicott St., 14203, Buffalo, NY, USA. alphy@buffalo.edu.
3
Department of Biochemistry and Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, 701 Ellicott St., 14203, Buffalo, NY, USA. jbard@buffalo.edu.
4
Department of Biochemistry and Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, 701 Ellicott St., 14203, Buffalo, NY, USA. bjmarzul@buffalo.edu.
5
Department of Biochemistry and Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, 701 Ellicott St., 14203, Buffalo, NY, USA. njnowak@buffalo.edu.
6
Department of Biochemistry and Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, 701 Ellicott St., 14203, Buffalo, NY, USA. mjbuck@buffalo.edu.

Abstract

BACKGROUND:

Integration of RNA-seq expression data with knowledge on chromatin accessibility, histone modifications, DNA methylation, and transcription factor binding has been instrumental for the unveiling of cell-specific local and long-range regulatory patterns, facilitating further investigation on the underlying rules of transcription regulation at an individual and allele-specific level. However, full genome transcriptome characterization has been partially limited by the complexity and increased time-requirements of available RNA-seq library construction protocols.

FINDINGS:

Use of the SX-8G IP-Star® Compact System significantly reduces the hands-on time for RNA-seq library synthesis, adenylation, and adaptor ligation providing with high quality RNA-seq libraries tailored for Illumina high-throughput next-generation sequencing. Generated data exhibits high technical reproducibility compared to data from RNA-seq libraries synthesized manually for the same samples. Obtained results are consistent regardless the researcher, day of the experiment, and experimental run.

CONCLUSIONS:

Overall, the SX-8G IP-Star® Compact System proves an efficient, fast and reliable tool for the construction of next-generation RNA-seq libraries especially for trancriptome-based annotation of larger genomes.

PMID:
25879881
PMCID:
PMC4391147
DOI:
10.1186/s13104-015-1089-9
[Indexed for MEDLINE]
Free PMC Article

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