GEO DataSets

(Submitter supplied) Three biological replicates of H. volcanii grown under optimal conditions to mid-exponential growth phase were used to determine the primary transcriptome and map 5’-ends of transcripts. In total, 4,749 potential transcriptional start sites (TSS) were detected. A position weight matrix was derived for promoter prediction, showing that 64% of the TSS were preceded by stringent or relaxed basal promoters. more...

Organism:

Haloferax volcanii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25010

6 Samples

Download data: WIG

(Submitter supplied) We demonstrate here the transcriptional landscape and functional roles of sRNAs specifically in the regulation of the oxidative stress response of the model haloarchaeon Haloferax volcanii. We sequenced 5 biological replicates of H. volcanii strain H53 under no challenge and oxidative stress (H2O2) conditions at mid-exponential phase (OD 0.4). Thousands of sRNAs, both intergenic and antisense, were discovered using strand-specific sRNA-seq, comprising around 30% of the transcriptome during non-challenged and oxidative stress conditions. more...

Organism:

Haloferax volcanii DS2

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21976

16 Samples

Download data: TXT

(Submitter supplied) Background: During the symbiosis with legumes, Bradyrhizobium japonicum cells infect roots where they induce the formation of root nodules and differentiate into intracellular nitrogen-fixing bacteroids. We used differential RNA-seq (dRNA-seq) for the genome-wide detection of transcriptional start sites (TSSs) in B. japonicum USDA 110 cells grown free-living or as bacteroids in soybean root nodules. more...

Organism:

Bradyrhizobium diazoefficiens USDA 110

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20219

4 Samples

Download data: WIG

(Submitter supplied) Background: Bacillus methanolicus MGA3 is a thermophilic, facultative ribulose monophosphate (RuMP) cycle methylotroph. Methylotrophy in this organism depends on the endogenous plasmid pBM19 although all ribulose monophosphate cycle enzymes are also encoded on the chromosome. Together with its ability to produce high yields of amino acids, the relevance of this microorganism as a promising and valuable candidate for future biotechnological applications is evident. more...

Organism:

Bacillus methanolicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19581

2 Samples

Download data: XLS

(Submitter supplied) The non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi is investigated using the RNA-seq technology. A dedicated computational pipeline analyzes RNA-seq reads and prior genome annotation to identify small RNAs, untranslated regions of mRNAs, and cis-encoded antisense transcripts. Unlike other archaea, such as Sulfolobus and Halobacteriales, P. abyssi produces few leaderless mRNA transcripts. more...

Organism:

Pyrococcus abyssi

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18745

1 Sample

Download data: GFF

(Submitter supplied) In this study transcriptional start sites (TSS) for H. pylori 26695 were determined

Organism:

Helicobacter pylori 26695

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19991 GPL19992

6 Samples

Download data: WIG

(Submitter supplied) Background: Prokaryotes have relatively small genomes, densely-packed and apparently dominated by protein-encoding sequences. However, data now generated by high throughput RNA sequencing (RNA-seq) reveal surprisingly more-complex transcriptomes with many previously unrecognized and unanticipated non-coding small and antisense transcripts. To date, such studies have investigated primarily Bacteria. more...

Organism:

Thermococcus kodakarensis KOD1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18473

5 Samples

Download data: WIG

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

Organism:

Shewanella sp. W3-18-1; Shewanella loihica PV-4; Shewanella amazonensis SB2B; Shewanella sp. MR-4; Shewanella sp. MR-7; Shewanella sp. ANA-3; Shewanella oneidensis MR-1; Shewanella putrefaciens CN-32

Type:

Expression profiling by genome tiling array; Expression profiling by high throughput sequencing

10 related Platforms

26 Samples

Download data: FTR, WIG

(Submitter supplied) We combined high-resolution tiling microarrays and 5'-end RNA sequencing to obtain a genome-wide map of transcription start sites (TSSs) for Shewanella oneidensis MR-1. To test the reliability of these TSSs, we compared our result to those from differential RNA sequencing (dRNA-seq), which discriminates primary and processed ends of transcripts. We found that our identified TSSs tend to have significantly more mapped reads in the TEX(+) sample than the TEX(-) sample. more...

Organism:

Shewanella oneidensis MR-1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18765

4 Samples

Download data: WIG

(Submitter supplied) 5' RNASeq of mRNA from Shewanella sp W3-18-1 grown aerobically in Luria-Bertani broth (LB) and defined lactate minimal medium

Organism:

Shewanella sp. W3-18-1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16843

2 Samples

Download data: WIG

(Submitter supplied) 5' RNASeq of mRNA from Shewanella amazonensis SB2B grown aerobically in Luria-Bertani broth (LB) and defined lactate minimal medium

Organism:

Shewanella amazonensis SB2B

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16842

2 Samples

Download data: WIG

(Submitter supplied) 5' RNASeq of mRNA from Shewanella loihica PV-4 grown aerobically in Luria-Bertani broth (LB) and defined lactate minimal medium

Organism:

Shewanella loihica PV-4

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16841

2 Samples

Download data: WIG

(Submitter supplied) 5' RNASeq of mRNA from Shewanella sp MR-7 grown aerobically in Luria-Bertani broth (LB) and defined lactate minimal medium

Organism:

Shewanella sp. MR-7

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16840

2 Samples

Download data: WIG

(Submitter supplied) 5' RNASeq of mRNA from Shewanella sp MR-4 grown aerobically in Luria-Bertani broth (LB) and defined lactate minimal medium

Organism:

Shewanella sp. MR-4

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16838

2 Samples

Download data: WIG

(Submitter supplied) 5' RNASeq of mRNA from S. oneidensis MR-1 grown aerobically in Luria-Bertani broth (LB) and defined lactate minimal medium

Organism:

Shewanella oneidensis MR-1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16837

3 Samples

Download data: WIG

(Submitter supplied) 5' RNASeq of mRNA from Shewanella putrefaciens CN-32 grown aerobically in Luria-Bertani broth (LB) and defined lactate minimal medium

Organism:

Shewanella putrefaciens CN-32

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16836

2 Samples

Download data: WIG

(Submitter supplied) 5' RNASeq of mRNA from Shewanella sp ANA-3 grown aerobically in Luria-Bertani broth (LB) and defined lactate minimal medium

Organism:

Shewanella sp. ANA-3

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16835

2 Samples

Download data: WIG

(Submitter supplied) High-resolution tiling analysis of the MR-1 transcriptome under diverse growth conditions The conditions include aerobic growth in Luria-Bertani broth (LB), aerobic growth in defined lactate minimal medium, anaerobic growth in defined lactate minimal medium with 20mM dimethyl sulfoxide as the electron acceptor, anaerobic growth in defined lactate minimal medium with 10mM iron (III) citrate as the electron acceptor, 10 minutes post heat shock at 42oC see GSE39468 for tiling data on lactate minimal media

Organism:

Shewanella oneidensis MR-1

Type:

Expression profiling by genome tiling array

Platform:

GPL16797

5 Samples

Download data: FTR

(Submitter supplied) Oxidative stress responsive small non-coding RNAs (sRNAs) have been reported in the model archaeon, Haloferax volcanii, but targets and mechanisms of actions have not been elucidated. While haloarchaea are highly resistant to oxidative stress, a comprehensive understanding of the mechanisms regulating this remarkable response is lacking. Here, using a combination of high throughput and reverse molecular genetic approaches we elucidated the functional role of the most up-regulated intergenic sRNA during oxidative stress in H. more...

Organism:

Haloferax volcanii DS2

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21976

16 Samples

Download data: TXT, XLSX

(Submitter supplied) Bacillus amyloliquefaciens FZB42 is a representative organism for Gram positive soil bacteria associated with plant roots and beneficial to plant growth. It is of immense importance to understand mechanisms of this class of bacteria adapting to rhizosphere. In this work employing differential RNA sequencing (RNA-seq) and Northern blot, we systematically identified transcription start sites of mRNAs as well as non-coding regulatory RNAs in FZB42. more...

Organism:

Bacillus velezensis FZB42

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19866

12 Samples

Download data: WIG