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Sample GSM3290597 Query DataSets for GSM3290597
Status Public on Dec 21, 2018
Title Col_Highlight_2min_Local Leaf_rep_1
Sample type SRA
 
Source name Col_Highlight_2min_Local Leaf
Organism Arabidopsis thaliana
Characteristics ecotype: Col
stress: Highlight
time (min): 2
repeat: 1
genotype: wild type
tissue: Local Leaf
Treatment protocol Local leaves of 4– to 5-week-old Col (WT) and rbohD plants were exposed to a light intensity of 2000 µmol m-2 sec-1 for periods of 0, 2, 4 and 8 min using a gooseneck light source (ACE I; Schott)
Growth protocol Arabidopsis thaliana Col (WT) and rbohD knockout plants were grown in peat pellets (Jiffy-7, Jiffy, http://www.jiffygroup.com/en/) at 23°C under short day growth conditions (8-hour light/16-hour dark, 50 µmol m−2 s−1).
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 Experiment1
Column name in processed data file: M3
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 files included 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)
GSE117296 Identification and characterization of a core set of ROS wave-associated transcripts involved in the systemic acquired acclimation response of Arabidopsis to excess light [Timecourse]
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 SAMN09688994
SRA SRX4403757

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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