|
| Status |
Public on Sep 29, 2024 |
| Title |
ruvcRNA1 |
| Sample type |
SRA |
| |
|
| Source name |
Cell precipitation
|
| Organism |
Ralstonia solanacearum |
| Characteristics |
tissue: Cell precipitation
genotype: RuvC mutant
|
| Treatment protocol |
Centrifugation at 12000 revolutions per minute (rpm) to collect bacterial cell precipitation and quick-frozen preservation
|
| Growth protocol |
Strains were grown on Casamino Acids-Peptone-Glucose (CPG) medium at 28℃ 190 revolutions per minute (rpm) to OD600=1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the frozen the cell precipitation with TRNzol reagent.
Libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq X Plus |
| |
|
| Data processing |
RNA extraction, library construction, sequencing , and analysis were performed by Beijing Novogene
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..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. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package 3.24.3). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as he threshold for significantly differential expression.
Assembly: ASM912v1 Ralstonia solanacearum
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Jun 25, 2024 |
| Last update date |
Sep 29, 2024 |
| Contact name |
Xinya Du |
| E-mail(s) |
duxinya9869@163.com, xinyadu@webmail.hzau.edu.cn
|
| Phone |
18602761757
|
| Organization name |
Huazhong Agricultural University
|
| Street address |
Huazhong Agricultural University, No. 1, Shishishan Street, Hongshan District
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL34644 |
| Series (1) |
| GSE270737 |
Holliday junction resolvase RuvC targets biofilm eDNA to facilitate pathogen spread in plants |
|
| Relations |
| BioSample |
SAMN42040285 |
| SRA |
SRX25052933 |
