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Sample GSM902873 Query DataSets for GSM902873
Status Public on Sep 01, 2014
Title CVL39 Selected sample D5 bisulfite
Sample type SRA
 
Source name CVL39 Selected sample
Organism Arabidopsis thaliana
Characteristics genotype: Recombinant inbred line CVL39
tissue: Whole above ground plant
age: 25 days
Treatment protocol Library prepared DNA was subjected to bisulfite treatment to convert unmethylated cytosines to thymines for bisulfite sequencing.
Growth protocol Sterilized seeds were initially sown on MA agar plates and stratified at 4°C for three days to ensure synchronised germination. After 12 days seedlings of CVL39 and CVL125 were transferred to pots in a general soil mix and grown under long-day conditions (23°C, 16 h light, 8 h dark). On day 25 the above ground parts of one individual were harvested in an Eppendorf tube containing glass beads and flash frozen in liquid nitrogen for DNA extraction.
Extracted molecule genomic DNA
Extraction protocol Using four micrograms of genomic DNA, a SOLIDTM fragment library for bisulfite genomic methylation profiling was prepared according to the manufacturer’s instructions Life technologiesTM with the following modifications. Both the P1-A and the P2-A adaptors consisted of 5-methyl-cytosines instead of cytosine, which ensures amplification of both the sense and antisense strands during emulsion PCR and avoids loss of unique molecules. After adaptor ligation and nick-translation, 500 ng of DNA was subjected to bisulfite conversion.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model AB SOLiD System 3.0
 
Description DNA methylome of 25-day-old plants which experienced 5 generations of selection and 2 generations without selection
Data processing SOCS V1.0 Alignment (Ondov et. al 2010, Bioinformatics, Volume 26, Issue 15, pages 1901-2), using recombinant genomes between Cvi/Ler Ecotypes
SOCS V1.0 Alignment gives the methylation statistics as number methylated and unmethylated cytosines per genomic position
Filter out positions which are covered by at least 4 and less than 50 reads
Apply Fisher's exact test to identify differentially methylated positions between the test samples (S2 samples) and the reference samples (A2 sample) for each genotype (_DMC4 Processed Data Files)
Genome_build: Arabidopsis TAIR10
 
Submission date Mar 27, 2012
Last update date May 15, 2019
Contact name Christian Heichinger
E-mail(s) christian.heichinger@uzh.ch
Phone 41-(0)44-634 8275
Organization name Zürich University
Department Institute of Plant Biology
Lab Developmental Genetics
Street address Zollikerstrasse 107
City Zürich
State/province Zürich
ZIP/Postal code 8008
Country Switzerland
 
Platform ID GPL10088
Series (2)
GSE36845 Selection of epigenetic variation in Arabidopsis [Bisulfite-Seq]
GSE36846 Selection of epigenetic variation in Arabidopsis
Relations
SRA SRX131922
BioSample SAMN00839775

Supplementary file Size Download File type/resource
GSM902873_CVL39_D5_DMC4.txt.gz 81.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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