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Sample GSM2111751 Query DataSets for GSM2111751
Status Public on Apr 07, 2017
Title trm4b rep2_roots
Sample type SRA
 
Source name 6 days after germination seedling roots grown on 1/2 MS media plates
Organism Arabidopsis thaliana
Characteristics cultivar: Col-0
genotype: trm4b-1
tissue: root
Growth protocol Roots were harvested from seedlings grown on 1/2 MS media plates
Extracted molecule total RNA
Extraction protocol RNA was extracted using the Spectrum Plant total RNA kit (SIGMA-ALDRICH) and contaminating DNA removed using DNAse (SIGMA-ALDRICH). Ribosomal RNA was depleted using Epicentre Ribo-Zero rRNA removal kits (Plant Seed/Root) and then bisulfite converted prior to library preparation
RNA libraries were prepared for sequencing using standard Illumina protocols except RNA fragmentation was not performed.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Description rRNA depleted RNA
RNA Bisulfite-seq
Processed data files: Supplementary_Table_2.xlsx and Supplementary_Table_3.xlsx
Data processing Library strategy: RNA Bisulfite-seq
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed to remove adaptor sequences, and filtered for low-quality reads using "Trimmomatic"
Trimmed reads were then globally mapped to in silico bisulfite converted Arabidopsis TAIR 10 reference genome using "TopHat"
Differential methylation and overall methylation calls were called using FDR 0.3 and methylation percentage greater than or equal to 1%
Genome_build: TAIR 10
Supplementary_files_format_and_content: excel file containing overall methylation calls (Supplementary_Table_2) and excel file containing wild type versus trm4b-1 differential methylation calls (Supplementary_Table_3). Processed data files are available on the SuperSeries (GSE80054) record.
 
Submission date Apr 07, 2016
Last update date May 15, 2019
Contact name Alice Louise Burgess
E-mail(s) alice.burgess@adelaide.edu.au
Organization name University of Adelaide
Department Genetics and Evolution
Lab Iain Searle Laboratory
Street address Frome road
City Adelaide
State/province SA
ZIP/Postal code 5005
Country Australia
 
Platform ID GPL13222
Series (2)
GSE80052 Transcriptome-wide RNA 5-methylcytosine methylation in roots of Arabidopsis thaliana
GSE80054 Transcriptome-wide RNA 5-methylcytosine methylation in siliques, shoots and roots and root gene expression profiling of Arabidopsis thaliana
Relations
BioSample SAMN04623246
SRA SRX1686953

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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