Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Definition of global transcriptional variation in wild type Pseudomonas fluorescens Pf0-1 and its phosphorothioate modification (PT) deficient mutant by RNA-seq analysis

ABSTRACT: 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.

ORGANISM(S): Pseudomonas fluorescens

PROVIDER: GSE110489 | GEO | 2018/02/15

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Expression analysis of the AdnA regulon in Pseudomonas fluorescens Pf0-1

Project description:Investigation of whole genome gene expression AdnA in Pseudomonas fluorescens, an ortholog of FleQ in P. aeruginosa, regulates both motility and flagella-mediated attachment to various surfaces. A whole genome microarray determined the AdnA transcriptome by comparing the gene expression pattern of wild-type Pf0-1 to that of Pf0-2x (adnA-) in broth culture. In the absence of AdnA, expression of 92 genes was decreased, while 11 genes showed increased expression. Analysis of 16 of these genes fused to lacZ confirmed the microarray results. Several genes were further evaluated for their role in motility and biofilm formation. Two genes, Pfl01_1508 and Pfl01_1517, affected motility and had different effects on biofilm formation in Pf0-1. These two genes are predicted to encode proteins similar to the glycosyl transferases FgtA1 and FgtA2, which have been shown to be involved in virulence and motility in P. syringae. Three other genes, Pfl01_1516, Pfl01_1572, and Pfl01_1573, not previously associated with motility and biofilm formation in Pseudomonas had similar affects on biofilm formation in Pf0-1. Deletion of each of these genes led to different motility defects. Our data revealed an additional level of complexity in the control of flagella function beyond the core genes known to be required, and may yield insights into processes important for environmental persistence of P. fluorescens Pf0-1.

2011-11-30 | GSE33865 | GEO

Fusarium sp. PT strain:PT

Project description:Fusarium sp. isolate PT

| PRJNA737353 | ENA

Pt-seq unveils the genomic binding pattern of platinum-based drugs [Pt-seq]

Project description:Platinum-based drugs (Pt drugs) are widely used in cancer chemotherapy, yet their genome-wide DNA binding patterns remain incompletely understood. Here, we present Pt-seq, an antibody-assisted, genome-wide method for mapping Pt-DNA adducts at single-base resolution. By employing exo- and endo- nucleases to remove background DNA, Pt-seq enables highly robust and sensitive profiling of binding sites for cisplatin, oxaliplatin, lobaplatin, and a Pt(IV) complex. Using Pt-seq, we identified hundreds to a few thousand binding clusters that are 10-20 kb in length and highly consistent among different Pt drugs. Notably, these binding clusters predominantly localize to centromeric and rDNA regions. In cisplatin-resistant cells, we found significantly reduced binding within these regions, suggesting a potential role in drug resistance. Moreover, we found that de novo mutations in cancer cells can create novel binding sites for Pt drugs. Based on this, we demonstrated that ICR-191, an acridine orange compound capable of inducing G insertions, enhances cisplatin-DNA crosslinking and sensitizes cells to Pt drugs. Collectively, Pt-seq sensitively profiles Pt drug-DNA interactions and deepens our understanding of the genome-wide effect of chemotherapeutic drugs.

2025-02-13 | GSE289501 | GEO

Expression analysis of the AdnA regulon in Pseudomonas fluorescens Pf0-1

2011-11-30 | E-GEOD-33865 | biostudies-arrayexpress

Pseudomonas fluorescens Pf0-1

Project description:Pseudomonas fluorescens Pf0-1 transcriptome - Pf0-1REa

| PRJNA439773 | ENA

Pseudomonas fluorescens Pf0-1

Project description:Pseudomonas fluorescens Pf0-1 transcriptome - Pf0-1REb

| PRJNA439774 | ENA

Pseudomonas fluorescens Pf0-1

Project description:Pseudomonas fluorescens Pf0-1 transcriptome - Pf0-1REc

| PRJNA439775 | ENA