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Sample GSM1388112 Query DataSets for GSM1388112
Status Public on May 17, 2014
Title Mature green stage embryo
Sample type SRA
 
Source name Arabidopsis mature green stage embryo
Organism Arabidopsis thaliana
Characteristics cultivar: ws-0
developmental stage: mature green seed
age: 13 DAP
tissue: embryo
Growth protocol Arabidopsis thaliana (L.) Heynh, ecotype Wassilewskja (ws-0) plants were grown under standard greenhouse conditions (Belmonte et al., PNAS 2013). Siliques were staged according to criteria described in methods of Belmonte et al. Whole seeds containing mature green stage embryos were collected. The embryo and seed coat were manually separated.
Extracted molecule genomic DNA
Extraction protocol Collected tissues 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 and 250 nanogram of genomic DNA isolated from embryo and seed coat, respectively, 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 EMB
Embryo from 13DAP seeds were collected.
Data processing Basecalls performed using RTA version 1.12.4.2.
Original data files from the Illumina sequencing pipeline were 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 (TAIR10) obtained from the TAIR website (http://www.arabidopsis.org/) 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: TAIR10
Supplementary_files_format_and_content: Tab-delimited text file including methylation level of each sampled cytosine. Column definitions are included in the supplementary README.txt file that is linked to the Series record.
 
Submission date May 16, 2014
Last update date May 17, 2014
Contact name Bob Goldberg
E-mail bobglab@mcdb.ucla.edu
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)
GSE57755 Methylation Changes in Arabidopsis Mature Green Seed Parts
Relations
BioSample SAMN02782464
SRA SRX545921

Supplementary file Size Download File type/resource
GSM1388112_At.wm.mg.emb.bsseq.chr1-5.perC.txt.gz 147.7 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data provided as supplementary file

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