|
Status |
Public on Dec 21, 2018 |
Title |
Col_H2O_Control_Systemic Leaf_rep2 |
Sample type |
SRA |
|
|
Source name |
Col_H2O_Control_Systemic Leaf
|
Organism |
Arabidopsis thaliana |
Characteristics |
ecotype: Col treatment: H2O repeat: 2 genotype: wild type stress: Control tissue: Systemic Leaf
|
Treatment protocol |
To inhibit the propagation of the ROS wave from the local to the systemic leaf, a drop of 0.3% agarose-containing water or 50 mM diphenyleneiodonium (DPI), was placed at the midpoint between the local and systemic leaves of 4– to 5-week-old Col-0 plants for 15 min. Local leaves of 4– to 5-week-old Col were exposed to a light intensity of 2000 µmol m-2 sec-1 for 8 min using a gooseneck light source (ACE I; Schott)
|
Growth protocol |
Arabidopsis thaliana Col (WT) 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 |
Column name in processed data file: ZM10
|
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 mean normalized counts for each sample
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|
|
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) |
GSE117298 |
Identification and characterization of a core set of ROS wave-associated transcripts involved in the systemic acquired acclimation response of Arabidopsis to excess light [DPI] |
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 |
SAMN09689092 |
SRA |
SRX4403824 |