|
| Status |
Public on Jan 18, 2021 |
| Title |
BE6_4 |
| Sample type |
SRA |
| |
|
| Source name |
bbc_Pst DC3000 D36E_6hpi
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype background: Col-0
genotype/variation: bbc
age: Four-week-old
treatment: Pst DC3000 D36E
time point: 6hpi
tissue: leaf
|
| Treatment protocol |
Four-week-old Arabidopsis plant leaves were infiltrated with Sterile water (Mock) or different Pst strains at OD600=0.04, and then harvested at indicated time points. Two leaves from different plants were collected as one sample and in total 4 samples were collected for each treatment.
|
| Growth protocol |
Plants were grown in soil in environmentally-controlled growth chambers, with relative humidity at 60% and temperature at 22℃ with 12/12h day/night photoperiod.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total mRNA was extracted from leaves using Trizol reagent. Total RNA was treated with DNase I to remove DNA, and purified RNA was recovered with RNeasy® MinElute™ Cleanup kit. A total amount of 1 μg RNA per sample was used as input material for library preparation and Illumina sequencing.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer’s recommendations and sequenced on Illumina Hiseq platform and 150 bp paired-end reads were generated.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Raw data (raw reads) of fastq format were firstly processed through CASAVA version 1.4 In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
TPM of each gene was calculated based on the length of the gene and reads count mapped to this gene, considering the effect of sequencing depth and gene length for the reads count at the same time.
Genome_build: ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR10_genome_release/
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
|
| |
|
| Submission date |
Dec 30, 2019 |
| Last update date |
Jan 18, 2021 |
| Contact name |
Minhang Yuan |
| E-mail(s) |
[email protected]
|
| Organization name |
Chinese Academy of Sciences
|
| Department |
Shanghai Institute of Plant Physiology and Ecology
|
| Lab |
Plant-microbe Interactions
|
| Street address |
Fenglin
|
| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL23157 |
| Series (1) |
| GSE142747 |
Genome-wide expression analysis of PTI and ETI responses in wild type and PRR-deficient Arabidopsis plants |
|
| Relations |
| BioSample |
SAMN13700121 |
| SRA |
SRX7478620 |
