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Sample GSM1664385 Query DataSets for GSM1664385
Status Public on Apr 22, 2015
Title Leaf
Sample type SRA
Source name Arabidopsis leaf
Organism Arabidopsis thaliana
Characteristics tissue: leaves
cultivar: ws-0
Growth protocol Arabidopsis thaliana (L.) Heynh, ecotype Wassilewskja (ws-0) plants were grown under standard greenhouse conditions (Belmonte et al., PNAS 2013). Siliques and seed stage were staged according to criteria described in methods of Belmonte et al. Whole seeds were collected for genomic DNA isolation.
Extracted molecule genomic DNA
Extraction protocol Collected seeds were quickly frozen in liquid nitrogen and ground to a fine powder using a mortar and pestle. Genomic DNA was isolated from the powder using the DNEASY Plant Mini kit (Qiagen, Valencia, CA) according to manufacturer’s instructions
Approximately 500 nanogram of genomic DNA isolated from seeds and leaves was subjected to library preparation following the methods of Hsieh et al. (Hsieh T-F et al. 2009. Science 324:1451-1454) with modifications. We spiked-in ~ three nanogram of unmethylated lambda DNA (Promega) to serve as a control for complete bisulfite conversion. Adapter-ligated genomic DNA was subjected to two rounds of bisulfite (BS) treatment using the EpiTect kit (Qiagen, Valencia, CA). BS-treated DNA was purified using AMpure XP beads (Beckman) and PCR-amplified for 10 cycles using ExTaq (EpiCentre) DNA polymerase. PCR-amplified DNA fragments were size selected using the AMpure XP beads (Beckman). Phi-X174 DNA was spiked in to the library by the sequencing facility before cluster formation and sequencing.
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2000
Description leaves from 4 week plant were collected.
Data processing Basecalls performed using RTA version
Original data file from the Illumina sequencing pipeline. Each lane of sequencing is attached as an individual compressed file. The sequence data are in the QSEQ format
We aligned the raw reads to a pre-processed reference genome using BS Seeker [Chen et al. BMC Bioinformatics (2010)] allowing for two mismatches. The pre-processed reference genome consisted of sequences from the Arabidopsis thaliana genome (TAIR 10) obtained from the TAIR website ( and Phi-X174 reference genome (GenBank: J02482).
Reads containing three consecutive methylation in the non-CG sites were removed, possibly representing non-converted cytosines (Cokus et al. Nature 2008). Clonal reads possibly arising during the PCR amplification step were collapsed into one read.
Methylation level of sampled cytosine was calculated as (methylated calls / (methylated calls + unmethylated calls))
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited text file including methylation level of each sampled cytosine
Submission date Apr 21, 2015
Last update date May 21, 2015
Contact name Bob Goldberg
Phone 310-825-3270
Organization name University of California, Los Angeles
Department Molecular, Cell and Developmental Biology
Street address 610 Charles E Young Drive East
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
Platform ID GPL13222
Series (1)
GSE68132 Methylation Changes in Arabidopsis seed development
SRA SRX1003159
BioSample SAMN03497747

Supplementary file Size Download File type/resource
GSM1664385_At.Ws0.wm.leaf.bsseq.chr1-5.perC.txt.gz 155.4 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data provided as supplementary file

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