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Series GSE97206 Query DataSets for GSE97206
Status Public on Aug 18, 2017
Title Paramutation of natural epialleles in tomato [sRNA]
Organisms Solanum lycopersicum; Solanum pimpinellifolium; Solanum pennellii; Solanum lycopersicum x Solanum pennellii
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary By using DNA methylation of introgression lines as a marker of past paramutation, we characterise in details the paramutation of the \textit{H06} locus in crosses between Solanum lycopersicum and a range of tomato relatives and cultivars. Paramutation of H06 depends on the timing of sRNA production and conforms to the RNA-directed model of paramutation. By scanning the methylomes of tomato introgression lines for shared regions of differential methylation, thousands of candidate regions for paramutation are identified. Analysing the segregation of the methylation patterns for a subset of these regions shows variations in the penetrance of paramutation-like interactions.
 
Overall design sRNA of M82, S. pennellii and their F1 for leaf/flower/pollen, sRNA for Micro-Tom and S. pimpinellifolium seedlings, methylome data of M82 and introgression lines IL1-1, IL2-5 and IL8-3
 
Contributor(s) Gouil Q
Citation(s) 29554868
Submission date Mar 29, 2017
Last update date May 31, 2019
Contact name Quentin Gouil
Organization name Walter and Eliza Hall
Department Epigenetics and Development
Lab Ritchie lab
Street address 1G Royal Parade
City Parkville
State/province VIC
ZIP/Postal code 3052
Country Australia
 
Platforms (6)
GPL9245 Illumina Genome Analyzer (Solanum lycopersicum)
GPL10777 Illumina Genome Analyzer (Solanum lycopersicum x Solanum pennellii)
GPL16345 Illumina HiSeq 2000 (Solanum lycopersicum)
Samples (31)
GSM2559653 M82 seedling rep1 sRNA-seq
GSM2559654 M82 seedling rep2 sRNA-seq
GSM2559655 IL1-1 seedling sRNA-seq
This SubSeries is part of SuperSeries:
GSE97247 Paramutation of natural epialleles in tomato
Relations
BioProject PRJNA381072
SRA SRP102806

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
GSE97206_H06_sRNA_F1.txt.gz 1.2 Kb (ftp)(http) TXT
GSE97206_H06_sRNA_M82.txt.gz 267 b (ftp)(http) TXT
GSE97206_H06_sRNA_penne.txt.gz 859 b (ftp)(http) TXT
GSE97206_sRNA_clusters_counts.txt.gz 3.7 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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