Transcriptomics

Dataset Information

239

Stallion sperm transcriptome as revealed by microarray analysis and RNA sequencing


ABSTRACT: Purpose: In order to understand the functional significance of sperm transcriptome in stallion fertility, the aim of this study was to generate a detailed body of knowledge about the sperm RNA profile that defines a normal fertile stallion. Methods: The 50 bp single-end ABI SOLiD raw reads were directly aligned with the horse reference sequence EcuCab2 using ABI aligner software (NovoalignCS version 1.00.09, novocraft.com) which uses multiple indexes in the reference genome, identifies candidate alignment locations for each primary read, and allows completion of the alignment. Results: Next generation sequencing (NGS) of total RNA from the sperm of two reproductively normal stallions generated about 70 million raw reads and more than 3 Gb of sequence per sample; over half of these aligned with the EcuCab2 reference genome. Altogether, 19,257 sequence tags with average coverage ≥1 (normalized number of transcripts) were mapped in the horse genome. Conclusion: The sequence of stallion sperm transcriptome is an important foundation for the discovery of transcripts of known and novel genes, and non-coding RNAs, thus improving the annotation of the horse genome sequence draft and providing markers for evaluating stallion fertility. Reproductively fertile Stallion sperm transcriptome as revealed by RNA sequencing

ORGANISM(S): Equus caballus  

SUBMITTER: Terje Raudsepp   Pranab Jyoti Das  Pranab J Das 

PROVIDER: E-GEOD-38725 | ArrayExpress | 2013-02-19

SECONDARY ACCESSION(S): SRP013752GSE38725PRJNA168502

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Stallion sperm transcriptome comprises functionally coherent coding and regulatory RNAs as revealed by microarray analysis and RNA-seq.

Das Pranab J PJ   McCarthy Fiona F   Vishnoi Monika M   Paria Nandina N   Gresham Cathy C   Li Gang G   Kachroo Priyanka P   Sudderth A Kendrick AK   Teague Sheila S   Love Charles C CC   Varner Dickson D DD   Chowdhary Bhanu P BP   Raudsepp Terje T  

PloS one 20130211 2


Mature mammalian sperm contain a complex population of RNAs some of which might regulate spermatogenesis while others probably play a role in fertilization and early development. Due to this limited knowledge, the biological functions of sperm RNAs remain enigmatic. Here we report the first characterization of the global transcriptome of the sperm of fertile stallions. The findings improved understanding of the biological significance of sperm RNAs which in turn will allow the discovery of sperm  ...[more]

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