Modulation effects of nitric oxide on thalidomide treated chicken embryo transcriptome

Purpose: The aim of this study is to analyse and compare the differentially expressed genes between nitric oxide treated and thalidomide treated chick embryos Methods: The trancriptome sequencing was performed using Illumina HiSeq 2500 ® platform. The sequence reads were aligned to the reference genome of chicken (Galgal4) downloaded from Ensembl Release 75 database. Alignment was performed using TopHat (v2.0.8) program to the Ensembl Release 75 gene model of chicken with default parameter settings. After alignment, Cuffdiff (v2.2.0) program was used for performing differential expression analysis. Pathway analysis of differentially expressed genes was performed using DAVID program. Heat maps were constructed using R package software 3.1.0. Overall design: The mRNA profiles of thalidomide and spermine NONOate pretreated 6th day of chick embryo were generated by deep sequencing, using Illumina HiSeq 2500 platform.