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Sample GSM1085246 Query DataSets for GSM1085246
Status Public on Mar 07, 2013
Title Gre_0
Sample type SRA
 
Source name leaf
Organism Arabidopsis thaliana
Characteristics cultivar: Gre_0
tissue: leaf
ecotype id: 7160
Extracted molecule genomic DNA
Extraction protocol DNA was isolated using a Qiagen Plant DNeasy kit (Qiagen, Valencia, CA) following the manufacturer’s recommendations.
Approximately one to three micrograms of genomic DNA was sonicated to ~100 bp using the Covaris S2 System using the following parameters: cycle number = 6, duty cycle = 20%, intensity = 5, cycles/burst = 200 and time = 60 seconds. Sonicated DNA was purified using Qiagen DNeasy minielute columns (Qiagen). Each sequencing library was constructed similar to genomic DNA libraries except the ligation was performed with methylated adapters provided by Illumina. Ligation products were purified with AMPure XP beads (Beckman) at a ratio of 1.8X of beads to sample. Up to 450 ng of ligated DNA was bisulfite treated using the MethylCode Kit (Invitrogen, Carlsbad, CA) following the manufacturer’s guidelines and then PCR amplified using Pfu Cx Turbo (Agilent, Santa Clara, CA) using the following PCR conditions (2 minutes at 95C, 4 cycles of 15 seconds at 98C, 30 seconds at 60C, 4 minutes at 72C and 10 minutes at 72C).
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina Genome Analyzer IIx
 
Data processing Methylated cytosine calls were made using the pipeline described in Lister et al. Human DNA methylomes at base resolution show widespread epigenomic differences. 2009. Nature
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab separated file of methylated cytosine positions
 
Submission date Feb 20, 2013
Last update date May 29, 2019
Contact name Joseph R Ecker
E-mail(s) ecker@salk.edu
Phone 8584534100
Organization name HHMI-Salk-Institute
Department Genomic Analysis Laboratory
Lab Ecker lab
Street address 10010 North Torrey Pines Road
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platform ID GPL11221
Series (1)
GSE43857 Patterns of Population Epigenomic Diversity in Arabidopsis thaliana (Methyl-Seq)
Relations
SRA SRX248668
BioSample SAMN02085918

Supplementary file Size Download File type/resource
GSM1085246_mC_calls_Gre_0.tsv.gz 122.8 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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