GEO DataSets

(Submitter supplied) To investigate the in vivo functions of RecJ and RecJ-like, we conducted transcriptome analyses on the wild-type (WT), drrecJ deletion mutant (△J), drrecJ-like deletion mutant (△J-like), and drrecJ-like/recJ double deletion mutant (△J/△J-like) strains. The results of the transcriptome analysis reveal a nuanced interplay between these two proteins in vivo, encompassing both overlapping and antagonistic functions. more...

Organism:

Deinococcus radiodurans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31018

4 Samples

Download data: TXT

(Submitter supplied) N 4-methylcytosine (4mC) is a natural DNA modification occurring in thermophiles and plays important roles in restriction-modification (R-M) systems in bacterial genomes. However, the precise location and sequence context of 4mC in the whole genome are limited. In this study, we developed an APOBEC3A-mediated deamination sequencing (4mC-AMD-seq) method for genome-wide mapping of 4mC at single-base resolution. more...

Organism:

Deinococcus radiodurans

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL31018

3 Samples

Download data: CSV

(Submitter supplied) In this study, we mapped the DdrO regulon in Deinococcus radiodurans by using two genome-scale approaches, ChIP-seq and RNA-seq analyses. These approaches were performed to find additional DdrO targets sites that were not predicted by previous in silico analyses. To our knowledge, we present here the first ChIP-seq analysis performed at the genome level in D. radiodurans. Alignments of DNA sequences extracted from ChIP-seq analysis were also performed to compare the consensus motif found to the predicted DdrO-binding motif. more...

Organism:

Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30214

41 Samples

Download data: TXT

(Submitter supplied) This study explores the regulatory network of a sRNA named PprS (previously Dsr2) in Deinococcus radiodurans R1. We compared the transcriptomes of two strains with and without exposure to 10 kGy acute ionizing radiation (IR): D. radiodurans R1 (wild-type) and a PprS knockdown mutant (PprSKD) that expresses ~2-fold less PprS compared to WT levels. Analysis of this RNAseq dataset demonstrated significant differential expression of several transcripts in both WT (34) and PprSKD (61) strains during recovery from IR. more...

Organism:

Deinococcus radiodurans

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL30231

18 Samples

Download data: GFF

(Submitter supplied) Purpose: The goal of this study is to explore the role of DqsR of D. radiodurans R1 in transcriptome profiling under oxidative and non-oxidative stresses. Methods: mRNA profiles of wild-type D. radiodurans R1 and DqsR knockout strain with 100 mM H2O2 treatment or not were generated by deep sequencing using IIllumina Solexa. Results: A total of 17.03 million (M) and 19.61 M clean reads were obtained from the wild-type R1 and mutant strains; of these, 14.81 M and 16.78 M reads were mapped to the genome, respectively. more...

Organism:

Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19650

8 Samples

Download data: TXT

(Submitter supplied) RNA-seq was used to analysis of mazEF toxin-antitoxin system mediated post-transcriptional inhibition through its endoribonuclease activity. DNA damage agents ,such as MMC, activates the mazEF system leading to cells growth arrest. In the present study, results reveal that a larger number of genes involved in amino acid and carbohydrate metabolism, ion transport and transcription was down-regulated in the wild-type compared with the mazEF-dr mutant.

Organism:

Deinococcus radiodurans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23271

4 Samples

Download data: XLSX

(Submitter supplied) In this study, we identified potential sRNA candidates in D. radiodurans by a whole transcriptome deep sequencing analysis, and confirm the expression of 31 sRNAs in D. radiodurans with Northern blotting analysis and RT-PCR. A total of 8 confirmed sRNAs showed differential expression during recovery after acute ionizing radiation (15 kGy).

Organism:

Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19650

2 Samples

Download data: TXT