|
| Status |
Public on May 17, 2021 |
| Title |
0.5mM As (V) treated rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
bacteria
|
| Organism |
Xanthomonas oryzae pv. oryzae |
| Characteristics |
strain: IXO1088
phase: exponential phase
treatment: treated [0.5mM As (V)]
|
| Treatment protocol |
Cells were grown-up to OD600=0.4; then cultures were treated with different concentrations of arsenate (0.5mM and 1mM) or arsenite (0.6mM) for 30 minutes. Culture without treatment was used as control. The cells were harvested by centrifugation at 6,000g for 5min for RNA isolation.
|
| Growth protocol |
Strains were grown in nutrient broth media at 28̊ C at 180 rpm to an OD600 of 1.0. One percent of the aliquot was added to the fresh media and grown-up to OD600=0.4; then cultures were treated with different concentrations of arsenate (0.5mM and 1mM) or arsenite (0.6mM) for 30 minutes.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The cells were harvested by centrifugation at 6,000g for 5min for RNA isolation and then lysed using Trizol reagent. Total RNA was isolated using Direct-zol RNA MiniPrep kit (Zymo Research Corporation, Orange, CA, USA)
The rRNA was removed using ‘si-tools Pan-prokaryote ribopool probes,’ and further library preparation was done using TruSeq Stranded RNA library prep kit. Prepared libraries were sequenced using Illumina HiSeq x10 platform, and 150-bp paired-end reads were generated.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
Cells treated with 0.5mM arsenate As (V)
|
| Data processing |
Basecalling,demultiplication and adaptor treaming was performed by Illumina HiSeq control software
Quality of raw reads was assessed by using FastQC tool
Clean reads that passed the quality filter were mapped to the reference genome (X. oryzae pv. oryzae IXO1088 accession number CP040687) using EDGE pro (version-1.3.1).
Differential gene expression analysis of treated samples with respect to control was performed using DESeq program.
Genome_build: NZ_CP040687
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
|
| |
|
| Submission date |
Dec 17, 2020 |
| Last update date |
May 19, 2021 |
| Contact name |
Prabhu B Patil |
| E-mail(s) |
[email protected]
|
| Organization name |
CSIR Institute of Microbial Technology Chandigarh
|
| Lab |
Bacterial Genomics and Evolution
|
| Street address |
Sector 39 A
|
| City |
Chandigarh |
| State/province |
Chandigarh |
| ZIP/Postal code |
160036 |
| Country |
India |
| |
|
| Platform ID |
GPL29508 |
| Series (1) |
| GSE163417 |
Discerning role of a functional arsenic resistance cassette in evolution and adaptation of a rice pathogen |
|
| Relations |
| BioSample |
SAMN17104051 |
| SRA |
SRX9697966 |
