|
Status |
Public on Apr 07, 2017 |
Title |
WT 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: wild type 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 |
SAMN04623230 |
SRA |
SRX1686914 |