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Sample GSM929634 Query DataSets for GSM929634
Status Public on May 11, 2012
Title Early maturation-stage embryonic axis
Sample type SRA
 
Source name Soybean early maturation-stage embryonic axis part
Organism Glycine max
Characteristics cultivar: Williams 82
developmental stage: early maturation stage
tissue: Embryonic axis from seeds 6.0 - 7.0 mm in length
Growth protocol Soybean plants (Williams 82) were grown under standard greenhouse conditions (Le et al., PNAS 2010). Whole seeds containing early-maturation (EM) stage embryos were collected. The embryo was dissected out of the seed coat and the axis was manually separated from the cotyledons of the EM-stage embryo.
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 one microgram of genomic DNA 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. Two libraries were constructed from genomic DNA isolated from seed coat. One library was spiked in ~ three nanogram of unmethylated lambda DNA as all other libraries; the other library was spiked in ~ three nanogram of methylated lambda DNA to serve as a control for over conversion (i.e. conversion of methylated cytosine to uracil) during the bisulfite conversion step. The methylated lambda DNA was generated by treating unmethylated lambda DNA with CpG Methyltransferase (New England BioLabs). 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 Embryonic axis from seeds 6.0 - 7.0 mm in length were collected.
Data processing Basecalls performed using RTA version 1.12.4.2
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 soybean genome (Glyma version 1.0.1) [Schmutz et al. Nature (2010)] obtained from the Phytozome website (http://phytozome.net), soybean chloroplast genome (GenBank: DQ317523), lambda reference genome (GenBank: J02459), 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: Glyma version 1.01
Supplementary_files_format_and_content: tab-delimited text file including methylation level of each sampled cytosine
 
Submission date May 10, 2012
Last update date May 23, 2013
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 GPL15008
Series (1)
GSE37895 Methylation Changes in Soybean Early Maturation Seed Parts
Relations
SRA SRX147556
BioSample SAMN00992206

Supplementary file Size Download File type/resource
GSM929634_wm.em.axis.bsseq.chr1-20.perC.txt.gz 1.1 Gb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data provided as supplementary file

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