|
| Status |
Public on Jan 20, 2017 |
| Title |
WS-FJ9-20 |
| Sample type |
SRA |
| |
|
| Source name |
Phosphate-solubilizing bacterium
|
| Organism |
Burkholderia multivorans |
| Characteristics |
strain: WS-FJ9
tissue: Rhizospheric bacterium
genotype: Wild type
|
| Treatment protocol |
Bacteria were cultured under three levels of soluble phosphate (0, 5 and 20 mM).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The bacterial cells were harvested and immediately frozen in liquid nitrogen for the next RNA extractionand. RNA was isolated with Trizol (Invitrogen, USA). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using strand specific Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The filtered reads were obtained from raw data of three levels of exogenous soluble phosphate treated WS-FJ9 by filtering out adaptors, N-proportion (> 10%) and low quality (Q ≤ 20) reads. The de novo assembly for each treatment was performed to generate transcript assembly by using Trinity method with optimized k-mer length of 25. Contigs were firstly assembled from clean reads by SOAP denove, and then further extended and assembled to long sequence denominated “unigenes”.
Gene expression in transcript was calculated by reads per Kb per million reads (RPKM) method. The RPKM value of each gene was used in the consequent differential gene expression analysis. Differentially expressed genes were identified between two pairs of transcripts (WS-FJ9-0 versus WS-FJ9-5, WS-FJ9-5 versus WS-FJ9-20) by Cuffdiff and rigorously detected based on the description by Audic and Claverie (FDR ≤ 0.001 and |log2Ratio| ≥ 1) .
Genome_build: NA
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for WS-FJ9-0_RPKM.txt, WS-FJ9-5_RPKM.txt and WS-FJ9-20_RPKM.txt.
|
| |
|
| Submission date |
Jan 18, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Qingwei Zeng |
| E-mail(s) |
qwzeng2@gmail.com
|
| Organization name |
Nanjing Forestry University
|
| Street address |
159 Longpan road
|
| City |
Nanjing |
| ZIP/Postal code |
210037 |
| Country |
China |
| |
|
| Platform ID |
GPL22941 |
| Series (1) |
| GSE93761 |
Phosphate solubilization and gene expression of phosphate-solubilizing bacterium Burkholderia multivorans WS-FJ9 under different levels of soluble phosphate |
|
| Relations |
| BioSample |
SAMN06241710 |
| SRA |
SRX2503730 |
