E-GEOD-38725 - Stallion sperm transcriptome as revealed by microarray analysis and RNA sequencing

Status
Released on 19 February 2013, last updated on 14 March 2013
Organism
Equus caballus
Samples (2)
Protocols (3)
Description
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
Experiment type
RNA-seq of coding RNA 
Contacts
Pranab Jyoti Das <pjdas@cvm.tamu.edu>, Pranab J Das, Terje Raudsepp
Citation
Stallion Sperm Transcriptome Comprises Functionally Coherent Coding and Regulatory RNAs as Revealed by Microarray Analysis and RNA-seq. Das PJ, McCarthy F, Vishnoi M, Paria N, Gresham C, Li G, Kachroo P, Sudderth AK, Teague S, Love CC, Varner DD, Chowdhary BP, Raudsepp T. , Europe PMC 23409192
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-38725.idf.txt
Sample and data relationshipE-GEOD-38725.sdrf.txt
Additional data (1)E-GEOD-38725.additional.1.zip
Links