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| Status |
Public on Feb 15, 2018 |
| Title |
Definition of global transcriptional variation in wild type Pseudomonas fluorescens Pf0-1 and its phosphorothioate modification (PT) deficient mutant by RNA-seq analysis |
| Organism |
Pseudomonas fluorescens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
To determine whether PT modifications are involved in the epigenetic control of specific genes, RNA-seq analysis was conducted to define global transcriptional changes in early log-phase cultures of wild-type pf0-1 and the PT modifacation related genes(dndBCDE) deletion mutant TT-5. Compared with wild-type pf0-1, a total of ten genes in TT-5 exhibited differential expression of greater than 2-fold (log2-ratio>1 or <-1, p-value<0.05, FDR≤0.001), including 6 up-regulated genes and 4 down-regulated genes (Table 1). Compared with pf0-1, the most significantly downregulated genes were dndBCDE themselves due to the in-frame deletion in TT-5. Of the 6 up-regulated genes, two are phage-related proteins (Pfl01_1169 and Pfl01_3496); the rest are genes encoding a putative membrane protein (Pfl01_0900), xanthine dehydrogenase (Pfl01_1797), N-acetylmuramoyl-L-alanine amidase (Pfl01_5657) and a hypothetical protein (Pfl01_2488). The transcription levels of the differentially expressed genes varied to different degrees and the genes belong to different COG groups.
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| Overall design |
Examination of global transcriptional variation in wild type P. fluorescens Pf0-1 and its phosphorothioate modification (PT) deficient mutant
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| Contributor(s) |
Tong T, Chen S |
| Citation(s) |
29531068 |
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| Submission date |
Feb 12, 2018 |
| Last update date |
May 17, 2018 |
| Contact name |
Lianrong Wang |
| E-mail(s) |
lianrong@whu.edu.cn
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| Organization name |
Wuhan University
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| Street address |
Bayi Road
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| City |
Wuhan |
| ZIP/Postal code |
430071 |
| Country |
China |
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| Platforms (1) |
| GPL24598 |
Illumina HiSeq 2000 (Pseudomonas fluorescens) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA433851 |
| SRA |
SRP132712 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE110489_RAW.tar |
140.0 Kb |
(http)(custom) |
TAR (of XLS) |
| GSE110489_WT-1-VS-TT-5-1.GeneDiffExp.xls.gz |
593.5 Kb |
(ftp)(http) |
XLS |
| GSE110489_WT-1-VS-TT-5-1.GeneDiffExpFilter.xls.gz |
1.4 Kb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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