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Sample GSM2384978 Query DataSets for GSM2384978
Status Public on Jan 09, 2017
Title WT
Sample type SRA
Source name whole seedling
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
tissue: seedling
age: 2 weeks
genotype/variation: wild type
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 Qiagen Plant DNeasy kit (Qiagen), starting from purified nuclei.
Libraries were constructed starting from 0.5 - 1 μg of genomic DNA, using the NEBNext DNA Sample PrepReagentSet1 (New England Biolabs), following the Illumina Genomic Sample Prep Guide (Illumina).
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina Genome Analyzer IIx
Description wild type
Data processing For image analysis and base calling, we used the Illumina OLB software version 1.8
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 against the Arabidopsis thaliana genome TAIR10 version using Bismark (Krueger et al. 2011, Bioinformatics). Duplicated reads were collapsed into one read.
Chloroplast sequences were used to estimate the bisulfite conversion. To account for non-converted DNA, we applied a correction according to (Lister et al. 2013 Science). Briefly, the number of methylated reads were decreased as: m*= max(0, m – nc) (where m* is the corrected number of methylated reads, m is the raw number of methylated reads, n is the total number of reads and c is the conversion rate).
Genome_build: TAIR10
Supplementary_files_format_and_content: For each genotype, the CX_Report generated by Bismark is reported (Krueger et al. 2011, Bioinformatics), after correction for non-converted DNA has been applied.
Submission date Nov 07, 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 GPL11221
Series (2)
GSE89591 DNA sequence properties that determine susceptibility to epiallelic switching [Bisulfite-Seq]
GSE89592 DNA sequence properties that determine susceptibility to epiallelic switching
BioSample SAMN05990857
SRA SRX2332403

Supplementary file Size Download File type/resource
GSM2384978_wt_processed.txt.gz 195.2 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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