|
| Status |
Public on Dec 21, 2018 |
| Title |
Col_2min_H2O2_seedling_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Col_2min_H2O2_seedling
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col
time (min): 2
treatment: H2O2
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: 2-50
|
| 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 |
SAMN09689074 |
| SRA |
SRX4403804 |
