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) Deinococcus radiodurans is an extremophilic microorganism that possesses a unique DNA damage repair system, conferring strong resistance to radiation, desiccation, oxidative stress, and chemical damage. Recently, we discovered that D. radiodurans possesses a N4-methylation (m4C) methyltransferase called M.DraR1, which recognizes the 5'-CCGCGG-3' sequence and methylates the second cytosine. Here, we revealed its cognate restriction endonuclease R.DraR1 and recognized that it is the only endonuclease specially for non-4C-methylated 5'-CCGCGG-3' sequence so far. 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: DNA methylation has a global impact on gene expression Methods: Gene expression profiles of D. radiodurans R1 wild type and ΔM.DraR1 strains were generated by deep sequencing using Illumina HiSeqTM2500. Results: RNA-seq was used for differential expression gene analysis between wild-type and ΔM.DraR1 strains. A total of 1158 genes (766 upregulated genes and 392 downregulated genes) were differentially expressed in ΔM.DraR1 strain. more...

Organism:

Deinococcus radiodurans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26971

4 Samples

Download data: XLSX

(Submitter supplied) We investigated an improved method that combines competitive PCR and microarray techniques. This approach allowed us to quantify specific bacterial groups mounted on DNA chips with accuracy close to that of real-time PCR, despite a measurement at the end point of PCR, and also to estimate the bacterial DNA content in sample DNA.

Organism:

Neisseria meningitidis; Porphyromonas gingivalis; Fusobacterium nucleatum; Clostridium beijerinckii; Lactobacillus gasseri; Tannerella forsythia; Bacteria; Acinetobacter baumannii; Escherichia coli; Staphylococcus aureus; Staphylococcus epidermidis; Bacillus cereus; Schaalia odontolytica; Fusobacterium nucleatum subsp. nucleatum; Treponema denticola; Cereibacter sphaeroides; Streptococcus gordonii; Streptococcus agalactiae; Enterococcus faecalis; Bifidobacterium adolescentis; Homo sapiens; Prevotella intermedia; Prevotella nigrescens; Campylobacter rectus; Helicobacter pylori; Pseudomonas aeruginosa; Aggregatibacter actinomycetemcomitans; Phocaeicola vulgatus; Capnocytophaga gingivalis; Deinococcus radiodurans; Streptococcus mutans; Streptococcus intermedius; Cutibacterium acnes

Type:

Other

Platform:

GPL25612

178 Samples

Download data: CSV

(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

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

Type:

Expression profiling by array

Platform:

GPL18898

2 Samples

Download data: GPR

(Submitter supplied) Transcriptional profiling of Deinococcus radiodurans comparing control wild type cells with bphPR deletion mutant were treated with MMC (5 μg/ml)

Organism:

Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

Type:

Expression profiling by array

Platform:

GPL18898

1 Sample

Download data: GPR, XLSX

(Submitter supplied) Transcriptional profiling of Deinococcus radiodurans comparing control wild type cells with bphPR deletion mutant

Organism:

Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

Type:

Expression profiling by array

Platform:

GPL18898

1 Sample

Download data: GPR, XLSX

(Submitter supplied) Transcriptional profiling of comparing wildtype strains with DR0199-deletion strains under normal growth conditions.

Organism:

Deinococcus radiodurans

Type:

Genome variation profiling by SNP array

Platform:

GPL9466

3 Samples

Download data: GPR, TXT

(Submitter supplied) Transcriptional profiling of Deinococcus radiodurans comparing control untreated wild type cells with wild type cells treated with 0.3M NaCl or 2M NaCl

Organism:

Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

Type:

Expression profiling by array

Platform:

GPL10060

16 Samples

Download data: GPR, TXT

(Submitter supplied) Transcriptional profiling of comparing wildtype strains with DR1790-deletion strains under normal growth contidions. Keywords: Genetic modification

Organism:

Deinococcus radiodurans

Type:

Expression profiling by array

Platform:

GPL9466

1 Sample

Download data: GPR

(Submitter supplied) Transcriptional profiling of Deinococcus radiodurans comparing control untreated wild type cells with wild type cells treated with 100 µM CdCl2.

Organism:

Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

Type:

Expression profiling by array

Platform:

GPL10060

32 Samples

Download data: GPR

(Submitter supplied) Transcriptional profiling of comparing wildtype strains with rpob 9-bp-deletion strains under normal growth contidions.

Organism:

Deinococcus radiodurans

Type:

Expression profiling by array

Platform:

GPL9466

2 Samples

Download data: GPR

(Submitter supplied) This bacterial genome encodes pyrroloquinoline quinone (PQQ) synthase enzyme required for the synthesis of PQQ in bacteria. The gene pqqE encoding PQQ synthase was annotated in Deinococcus radiodurans R1 genome and synthesis of PQQ was shown in this bacterium. PQQ roles as an antioxidant and as an inducer of protein kinase in bacterial system was shown. The pqqE disuption mutant showed several folds decrease in gamma radiation tolerance of wild type cells and strong impairment of DSB repair. more...

Organism:

Deinococcus radiodurans; Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

Type:

Expression profiling by array

Platform:

GPL8947

2 Samples

Download data: GPR

(Submitter supplied) Bacterial cells lacking pyrroloquinoline quinone (PQQ) were sensitive to gamma radiation as compared to wild type cells. Deinococcus radiodurans genome encode for five putative PQQ binding STK domain-containing proteins. The comparison of gamma radiation response of all five-deletion mutants with wild type suggested that dr2518 mutant was hypersensitive to gamma radiation as compared to wild type and other mutants. more...

Organism:

Deinococcus radiodurans; Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

Type:

Expression profiling by array

Platform:

GPL8947

2 Samples

Download data: GPR