GEO DataSets

(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) 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) 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 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 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) 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

(Submitter supplied) Deinococcus radiodurans exposed to higher doses of gamma radiation showed induced levels of DRB0091 polypeptide annotated as a putative response regulator in an operon expressing upstream to DRB0090, histidine kinase. Deletion of drB0090 generated, showed decreased tolerance to DNA damage and impairment in DSB repair. Recombinant DR0090 protein showed phosphotransferase activity on its cognate response regulator, DRB0091. more...

Organism:

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

Type:

Expression profiling by array

Platform:

GPL8947

2 Samples

Download data: GPR

(Submitter supplied) see manufacturer's website (MYcroarray.com)

Organism:

Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

3 Series

2 Samples

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(Submitter supplied) 1. PCR produts are arrayed in 96-well round-bottom plates. Each well contains 500ng/ul of PCR products in DW 2. Mix with 5μL of PCR products in DW and 5μL of DMSO into 384-well, Genetix polystyrene V-bottom plates (cat# X6004) 3. Seal plates with Corning seals. 4. Incubate at 37℃ for 30 minutes to aid resuspension of DNA 5. Shake plates near maximum rotational speed on flat-bed shaker for 1 minute. 6. Centrifuge plates at 2000 rpm for 3minutes. 7. Remove seals and cover with plate lids. Place plates and slides(Corning GAPSII) in microarrayer 8. Start printing slides according to microarrayer manual 9. After the print run, put out 2 microarray slides from microarrayer and prescan them with microarray scanner for spot QC 10. All microarray slide is preformed UV-cross linking to immobilize spotted DNA at 200mJ of UV energy 11. Spotted cDNA microarrays are packed in slide case and deposited in dessicator

Organism:

Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

2 Series

48 Samples

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