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Series GSE80309 Query DataSets for GSE80309
Status Public on Dec 01, 2021
Title Transcriptome sequencing of thalidomide treated limb bud of chick embryo
Organism Gallus gallus
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: The aim of this study was to compare the differentially expressed genes under thalidomide treatment in limb buds.
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 81 database. Alignment was performed using STAR (version 2.4.2a ). Expression estimation carried out using cufflinks program (version 2.2.1).Differential expression analysis carried using the cuffdiff program in cufflinks(version 2.2.1). Heat maps were generated for gene expression analysis using R statistical software.
 
Overall design The mRNA profiles of thalidomide and vehicle control treated limb buds isolated from HH22 stage chick embryo were generated by deep sequencing, using Illumina HiSeq 2500 platform.
 
Contributor(s) kumar P, Gupta R, Chatterjee S
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Apr 14, 2016
Last update date Dec 02, 2021
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 (2)
GSM2124067 Limb Bud Vehicle control
GSM2124068 Limb Bud Thalidomide
Relations
BioProject PRJNA318534
SRA SRP073339

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
GSE80309_RAW.tar 2.7 Mb (http)(custom) TAR (of XLS)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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