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Series GSE202715 Query DataSets for GSE202715
Status Public on Sep 27, 2023
Title Dissecting the Dynamic Changes of Methylome and Transcriptome During Rice Transformation
Organism Oryza sativa
Experiment type Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary During transformation, tissue culture often carries epigenetic and genetic changes underlying somaclonal variations, leading to unpredictable phenotypes. Transformation treatments may individually and jointly contribute to somaclonal variations, but their specific impacts on rice epigenomes have never been examined. Here, we examined the changes in methylomes and transcriptomes associated with each of the components with different combinations of treatments. We found that individual transformation components targeted specific gene sets. When T-DNA was integrated, the pathway of secondary metabolism was activated, whereas primary metabolism was repressed. The transformation treatments resulted in global hypomethylation at CHH sites enriched at promoters highly associated with downregulation. The promoters that colocalized with miniature inverted-repeat TEs (MITEs) were found to be associated with epigenetic responses to stress, and this was not observed at sites without MITEs. Our results demonstrated component-specific epigenetic regulation related to adaptation to the stress response during rice transformation.
Overall design We performed whole-genome bisulfite sequencing (WGBS) and RNA-seq to examine DNA methylation and expression in a total of nine transformation components in TNG67 with two biological replicates of leave samples
Contributor(s) Hsieh JA, Chang P, Kuang L, Hsing YC, Chen P
Citation(s) 37394940
Submission date May 11, 2022
Last update date Sep 28, 2023
Contact name Ying-Chung Lin
Organization name National Taiwan University
Department Life Science
Street address NO. 1, SEC. 4, ROOSEVELT RD., DA-AN DIST.
City Taipei
ZIP/Postal code 10617
Country Taiwan
Platforms (1)
GPL19290 Illumina HiSeq 2500 (Oryza sativa)
Samples (36)
GSM6131723 Seedling BS-seq rep1
GSM6131724 Seedling BS-seq rep2
GSM6131725 Callus BS-seq rep1
BioProject PRJNA837100

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Supplementary file Size Download File type/resource
GSE202715_RAW.tar 8.7 Gb (http)(custom) TAR (of CGMAP)
GSE202715_RNAseq_FPKM_orcid_2hyxq6Ii.txt.gz 2.3 Mb (ftp)(http) TXT
GSE202715_RNAseq_RAW_count_orcid_2hyxq6Ii.txt.gz 1.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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