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Series GSE129110 Query DataSets for GSE129110
Status Public on Dec 01, 2021
Title Reduced representation bisulphite sequencing of two chickpea genotypes to identify differential DNA methylation patterns associated with drought tolerance and sensitivity
Organism Cicer arietinum
Experiment type Methylation profiling by high throughput sequencing
Summary In this study, to obtain a clear picture of drought mechanism involved in two distinctive chickpea genotype, the aim was to identify the DNA methylation patterns which potentially regulate drought tolerance/sensitivity of these selected genotypes. The leaf tissues from the shoot apical meristem from drought sensitive and drought tolerant genotypes were used for RRBS (Reduced representation bisulphite sequencing) under drought stress. The sequencing data was analysed using Bismark and methylkit to recall the methylation levels in control and samples for both genotypes and identify differentially methylated regions.
 
Overall design In our present study, RRBS sequencing was employed to identify drought-responsive differentiaton in differential methylation in chickpea leaf tissue of two genotypes ICC8261 and ICC283 to identify Differentially methylated regions related to biological, cellular and molecular pathways related to drought tolerance under drought stress. The significant methylation level difference observed between the two genotypes in shoot apical meristem leaves indicates how drought stresses affect the different mechanisms in both genotypes. In this study the emphasis was on how the regulation of epignetic modification such as DNA methylation were influenced by drought stress in the two genotypes as well as role of methylation in different context CpG,CHH,CHG.
 
Contributor(s) Mantri N, Badhan S
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Apr 01, 2019
Last update date Dec 02, 2021
Contact name Nitin Mantri
E-mail(s) nitin.mantri@rmit.edu.au
Phone +61 3 9925 7152
Organization name RMIT University
Department Biosciences and Food Technology
Street address 264 Plenty Rd, Bundoora VIC 3083
City Melbourne
State/province Victoria
ZIP/Postal code 3083
Country Australia
 
Platforms (1)
GPL26370 Illumina HiSeq 3000 (Cicer arietinum)
Samples (12)
GSM3693430 ICC283 Genotype control 1
GSM3693431 ICC283 Genotype control 2
GSM3693432 ICC283 Genotype control 3
Relations
BioProject PRJNA530151
SRA SRP189992

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
GSE129110_RAW.tar 269.1 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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