|
| Status |
Public on Apr 07, 2017 |
| Title |
WT 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: wild type
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 |
SAMN04623243 |
| SRA |
SRX1686950 |
