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Series GSE69159 Query DataSets for GSE69159
Status Public on Jan 01, 2017
Title Modulation effects of nitric oxide on thalidomide treated chicken embryo transcriptome
Organism Gallus gallus
Experiment type Expression profiling by high throughput sequencing
Summary 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.
Contributor(s) Veeraiah V, Chatterjee S
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Submission date May 22, 2015
Last update date May 15, 2019
Contact name Ravi Gupta
Organization name SciGenom Labs Pvt. Ltd.
Department Bioinformatics
Street address Plot no: 43A,SDF, 3rd floor, A Block,CSEZ, Kakkanad
City Cochin
State/province Kerala
ZIP/Postal code 682037
Country India
Platforms (1)
GPL19005 Illumina HiSeq 2500 (Gallus gallus)
Samples (4)
GSM1694113 Control
GSM1694114 Thalidomide
GSM1694115 Spermine NONOate
BioProject PRJNA284676
SRA SRP058621

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE69159_GeneExpression.xls.gz 2.6 Mb (ftp)(http) XLS
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Raw data are available in SRA
Processed data are available on Series record

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