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Sample GSM2393135 Query DataSets for GSM2393135
Status Public on Jan 04, 2017
Title ibm11_Ler_1st
Sample type SRA
Source name rosette leaves
Organism Arabidopsis thaliana
Characteristics ecotype: Ler-0
tissue: rosette leaves
age: 3 weeks
Growth protocol Plants were grown in plates under long-day conditions (21°C, 16 h light, 8 h dark)
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted using the Plant DNeasy kit (Qiagen) following the manufacturer's instructions.
Libraries were constructed starting from 150 ng of genomic DNA, using the EZ-DNA Methylation-Gold Kit (Zymo Research), following by DNA library preparation with the TruSeq DNA methylation kit (Illumina), according to manufacturer's instructions.
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina NextSeq 500
Description ibm1-1 mutant 1st generation
Data processing The raw reads were trimmed using Trimmomatic (Bolger et al, 2014 Bioinformatics) in order to remove adapter sequences. Reads with an average quality value of at least 15 in a window of 4 nucleotides were trimmed from both ends. After trimming, reads shorter than 16 bases were discarded.
The remaining sequences were aligned using Bismark (Krueger et al. 2011, Bioinformatics) against the Arabidopsis thaliana genome TAIR10 version or the PacBio Ler-0 genome assembly ( for Col-0 ibm1 or Ler-0 ibm1 mutant, respectively. Duplicated reads were collapsed into one read.
Chloroplast sequences were used to estimate the bisulfite conversion.
Genome_build: Arabidopsis thaliana Col-0: TAIR10; Ler-0: PacBio assembly (
Supplementary_files_format_and_content: For each genotype, the CX_Report generated by Bismark is reported (Krueger et al. 2011, Bioinformatics).
Submission date Nov 16, 2016
Last update date May 15, 2019
Contact name Marco Catoni
Organization name University of Birmingham
Department School of Biosciences
Street address Edgbaston
City Birmingham
ZIP/Postal code B15 2TT
Country United Kingdom
Platform ID GPL19580
Series (1)
GSE89913 Cytosine methylation at CpCpG sites triggers accumulation of non-CpG methylation in gene bodies
BioSample SAMN06020411
SRA SRX2352823

Supplementary file Size Download File type/resource
GSM2393135_ibm11_Ler_1st.CXreport.txt.gz 226.9 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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