|
| Status |
Public on Apr 07, 2017 |
| Title |
trm4b rep1_root_RNA-seq |
| 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
treatment: control conditions
|
| Treatment protocol |
Plants were either grown on media without paraquat, or with 0.01 uM paraquat
|
| 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) prior to library preparation
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
rRNA depleted RNA
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
RNA-seq data was adaptor-trimmed using "Trimmomatic"
Trimmed reads were mapped to the Arabidopsis TAIR10 reference genome using "TopHat"
Diferentially expressed genes were detected using "Limma"
Genome_build: TAIR 10
Supplementary_files_format_and_content: excel file with differential expressed genes from all comparisons from "Limma". File is available on series (GSE80053) 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) |
| GSE80053 |
Gene expression analysis (RNA-seq) of Arabidopsis thaliana roots in wild type and trm4b-1 mutants under control and oxidative stress conditions |
| GSE80054 |
Transcriptome-wide RNA 5-methylcytosine methylation in siliques, shoots and roots and root gene expression profiling of Arabidopsis thaliana |
|
| Relations |
| BioSample |
SAMN04623233 |
| SRA |
SRX1686917 |
