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Sample GSM852278 Query DataSets for GSM852278
Status Public on Dec 22, 2011
Title Late-maturation stage whole seed biological replicate 1
Sample type SRA
 
Source name Soybean seeds containing late-maturation (AA1) stage embryos
Organism Glycine max
Characteristics cultivar: Williams 82
Growth protocol Soybean plants (Williams 82) were grown under standard greenhouse conditions (Le et al., PNAS 2010). Whole seeds containing globular (GLOB) stage, cotyledon (COT), early- (EM), mid- (MM), and late- (LM) maturation, pre-dormancy (PD1 and PD2) stage embryos were collected. Whole dry (DRY) seeds containing dormant embryos were also collected. For seedlings, seeds were sown on soil and after six days after imbibition, the whole seedlings and the cotyledons of seedling were manually collected.
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. 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 Whole seeds 1.2 - 1.5 cm in length and have a fresh weight between 230 - 350 mg were collected. The entire embryo is yellow including the axis and cotyledons.
Data processing Raw: Original unprocessed and unfiltered data file from the Illumina sequencing pipeline. The raw data was converted to the FASTQ format using custom perl scripts. Each lane of sequencing is attached as an individual compressed file. The sequence data are in the FASTQ format.
Alignment: 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.
 
Submission date Dec 21, 2011
Last update date Jun 09, 2015
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)
GSE34637 Methylation Changes During Soybean Seed Development
Relations
SRA SRX113254
BioSample SAMN00768942

Supplementary file Size Download File type/resource
GSM852278_wm.aa1.seed.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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