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Sample GSM2111753 Query DataSets for GSM2111753
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

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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