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Sample GSM3290643 Query DataSets for GSM3290643
Status Public on Dec 21, 2018
Title Col_0min_H2O_seedling_rep1
Sample type SRA
 
Source name Col_0min_H2O_seedling
Organism Arabidopsis thaliana
Characteristics ecotype: Col
time (min): 0
treatment: H2O
repeat: 1
genotype: wild type
tissue: seedlings
Treatment protocol H2O2 treatment was conducted by adding 1 mM H2O2 to 5-day-old Col seedlings growing in 0.5 × MS media. Distilled water was added to control seedlings at time point 0. Seedlings were immediately frozen in liquid nitrogen after 2, 4 and 8 min of H2O2 treatment. About 100-150 seedlings were used for each time point and the experiment was repeated three times.
Growth protocol Col-0 seedlings were grown in 100 mL of sterile 0.5 × MS media on a shaker under constant light (50 µmol m-2 sec-1) for 5 days
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using Trizol (Invitrogen Life Technologies) according to the manufacturer’s instructions and purified using NucleoSpin RNA Clean-up kit (Macherey-Nagel).
TruSeqHT
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description Column name in processed data file: 2-49
Data processing Basecalling performed using Standard Illumina Base Caller (Bustard)
Quality control of reads were performed using FastQC v0.11.7
RNA-seq reads were aligned to Arabidopsis thaliana genome obtained from TAIR using STAR aligner v2.4.0.1
Differential gene expression analysis was performed using DeSeq2 v1.20.0
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-deliminated file includes mean normalized counts for each sample
 
Submission date Jul 18, 2018
Last update date Dec 21, 2018
Contact name Soham Sengupta
Organization name St. Jude Children's Research Hospital
Street address 262 Danny Thomas Place
City Memphis
State/province TN
ZIP/Postal code 38105
Country USA
 
Platform ID GPL19580
Series (2)
GSE117297 Identification and characterization of a core set of ROS wave-associated transcripts involved in the systemic acquired acclimation response of Arabidopsis to excess light [H2O2]
GSE117300 Identification and characterization of a core set of ROS wave-associated transcripts involved in the systemic acquired acclimation response of Arabidopsis to excess light
Relations
BioSample SAMN09689075
SRA SRX4403803

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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