Spermatonial stem cells (SSCs) are the foundation of spermatogenesis. Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs with at least 200 bp in length, which play important roles in various biological processes. Growth factor glial cell line-derived neurotrophic factor (GDNF), secreted from testis niches, is critical for self-renewal of SSCs in vitro and in vivo. Using Illumina HiSe...

The sea cucumber (Apostichopus japonicus) occupies a basal position during the evolution of deuterostomes and is also an important aquaculture species. In order to identify more immune effectors, transcriptome sequencing of A. japonicus coelomocytes in response to lipopolysaccharide (LPS) challenge was performed using the Illumina HiSeq™ 2000 platform. One hundred and seven differentially expre...

Ramie (Boehmeria nivea (L.) Gaud.) is a traditionally terrestrial fiber crop. However, hydroponic technology can enhance the quantity and quality of disease free Ramie plant seedlings for field cultivation. To date, few studies have attempted to examine the hydroponic induction of ramie roots and the molecular responses of ramie roots to aquatic environment. In this study, ramie tender stems wa...

BACKGROUND The tremendous output of massive parallel sequencing technologies requires automated robust and scalable sample preparation methods to fully exploit the new sequence capacity. METHODOLOGY In this study, a method for automated library preparation of RNA prior to massively parallel sequencing is presented. The automated protocol uses precipitation onto carboxylic acid paramagnetic be...

Since chloroplasts and mitochondria are maternally inherited and have unique features in evolution, DNA sequences of those organelle genomes have been broadly used in phylogenetic studies. Thanks to recent progress in next-generation sequencer (NGS) technology, whole-genome sequencing can be easily performed. Here, using NGS data generated by Roche GS Titanium and Illumina Hiseq 2000, we perfor...

As whole-genome sequencing becomes commoditized and we begin to sequence and analyze personal genomes for clinical and diagnostic purposes, it is necessary to understand what constitutes a complete sequencing experiment for determining genotypes and detecting single-nucleotide variants. Here, we show that the current recommendation of ∼30× coverage is not adequate to produce genotype calls acro...

Jeju horse (Natural Monument number 347) is a breed of horse that has experienced long-term isolation and domestication in Jeju Island, South Korea. We evaluated genetic features of this breed, including SNP, by whole-genome resequencing using an Illumina HiSeq 2000. A total of 5,986,852 SNP were identified in 4 Jeju horses and were divided into homozygous and heterozygous SNP (2,357,099 and 3,...

This article describes how the proteomic and transcriptomic data were produced during a study of the reproductive proteins of Pomacea maculata, an aquatic apple snail laying colorful aerial eggs, and provides public access to the data. The data are related to a research article titled 'An integrated proteomic and transcriptomic analysis of perivitelline fluid proteins in a freshwater gastropod ...

Peripheral γδ T cells in mice are classified into two major subpopulations, Vγ1+ and Vγ4+, based on the composition of T cell receptors. However, their intrinsic differences remain unclear. In this study, we analyzed gene expression profiles of the two subsets using Illumina HiSeq 2000 Sequencer. We identified 1995 transcripts related to the activation of Vγ1+ γδ T cells, and 2158 transcripts r...