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Sample GSM5928734 Query DataSets for GSM5928734
Status Public on Feb 17, 2023
Title h1ddm1.f9_1.bsseq
Sample type SRA
 
Source name rosette leaf
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
tissue: rosette leaf
Growth protocol Arabidopsis were sown to soil, stratified for 4 days at 4degC and transferred to controlled environment chambers where they were grown in 16h light / 8hr dark at 20deg C.
Extracted molecule genomic DNA
Extraction protocol DNA was isolated by pulverizing ~0.5 g of flash frozen rosette leaves of 4 week post-germination plants. ~100 mg of resulting powder was used to extract genomic DNA (gDNA) with the DNeasy plant mini kit (Qiagen cat. no. 69104) per manufacturer's instructions. gDNA was subsequently sonicated with the Bioruptor Pico (Diagenode) to ~250 bp median fragment length using 10 cycles of 30 seconds on and off. Agencourt Ampure beads (referred to as “beads” henceforth, cat. no. A63881) were then used at 2X volume to purify the sheared DNA.
Following ligation of methylated Truseq sequencing adapters (Illumina) to sheared DNA, bisulfite conversion of DNA was carried out according to manufacturer’s protocol (Qiagen Epitect Kit, cat. no. 59104) except without using carrier RNA. DNA was purified twice with 1.2X beads and converted a second time to ensure complete bisulfite conversion of unmethylated cytosine. Libraries were constructed using NEBnext kits (NEB cat. no. E7645) or Nugen/Tecan Ovation Ultralow (cat. no. 0344NB-08) following the manufacturer's instructions. NEB next indexing primers (cat. no. E7335S) were used for generating multiplexed libraries during PCR amplification of libraries.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2500
 
Data processing Bisulfite libraries were mapped to the genome following adaptor trimming with trim_galore (https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md) using BSMAP (Xi and Li 2009) using default settings for all analyses, except single-read analyses, for which we used Bismark (Kruger and Andrews 2011).
BSMAP output was converted to per-base methylation scores with BSMAP's methratio.py script using the -r setting to remove PCR duplicates.
Methratio.py output was converted to GFF and further processed and analysed using commands and workflows outlined in https://github.com/dblyons/modeling_h1ddm1/
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-seperated methratio.py output: chromosome, position, strand, cytosine context, ratio eff_CT_count, C_count, CT_count, rev_G_count, rev_GA_count, CI_lower, CI_upper.
 
Submission date Mar 01, 2022
Last update date Feb 19, 2023
Contact name David B. Lyons
E-mail(s) davidbrucelyons@gmail.com
Organization name John Innes Centre
Department Cell and Developmental Biology
Lab Daniel Zilberman
Street address Colney Lane
City Norwich
State/province Norfolk
ZIP/Postal code NR47UH
Country United Kingdom
 
Platform ID GPL17639
Series (1)
GSE197718 A balance of de novo and maintenance activities governs epigenetic inheritance of CG methylation in Arabidopsis transposons
Relations
BioSample SAMN26365688
SRA SRX14338982

Supplementary file Size Download File type/resource
GSM5928734_h1ddm1.f4_2.pe.methratio.tsv.gz 310.2 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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