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Sample GSM5928751 Query DataSets for GSM5928751
Status Public on Feb 17, 2023
Title h1ddm1_3_f3.rna
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 total RNA
Extraction protocol Rosette leaves from the F3 generation were flash frozen in liquid nitrogen, pulverized with mortar and pestle on dry ice, and the resulting material was subjected to vortexing in Trizol (Invitrogen, cat. no. 15596-026). Chloroform was then added at one-fifth the total volume and further vortexing was carried out until the solution appeared homogenous. RNA was subsequently pelleted in ice-cold isopropanol. The resuspended RNA was subjected to rRNA removal with Ribo-zero plant kit (Illumina, MRZPL1224) according to the manufacturer’s protocol.
50ng ribo-depleted was used for library preparation with the Scriptseq kit (Epicentre, cat. no. SSV21124) following the manufacturer’s protocol but with the following modifications: the RNA fragmentation step was extended to 10 minutes, and the temperature was increased to 90°C.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
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 SAMN26365671
SRA SRX14338961

Supplementary file Size Download File type/resource
GSM5928751_h1.rep3.abundance.tsv.gz 605.1 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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