GEO DataSets

(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) 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) 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) Background Bacteria rely on efficient gene regulatory mechanisms to switch between genetic programs when they are facing new environments. Although this regulation can occur at many different levels, one of the key steps is the initiation of transcription. Identification of the first nucleotide transcribed by the RNA polymerase is therefore essential to understand the underlying regulatory processes, since this provides insight on promoter strength and binding sites for transcriptional regulators, and additionally reveals the exact 5' untranslated region of the transcripts, which often contains elements that regulate translation. more...

Organism:

Klebsiella aerogenes; Acinetobacter baumannii; Staphylococcus aureus; Staphylococcus epidermidis

Type:

Expression profiling by high throughput sequencing; Other

4 related Platforms

30 Samples

Download data: TSV

(Submitter supplied) We show the transcriptomic landscape of the H2-producing archaeon Thermococcus onnurineus NA1 in response to different growth conditions using primary and whole transcriptome sequencing. We identified 1,082 purine-rich transcription initiation sites along with well-conserved TATA boxes, A-rich B recognition elements (BREs), and promoter proximal element (PPE) motifs in promoter regions, a high pyrimidine nucleotide content (T/C) at the −1 position, and Shine-Dalgarno (SD) motifs (GGDGRD) in 5' untranslated regions (5' UTRs). more...

Organism:

Thermococcus onnurineus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL22336 GPL22337

7 Samples

Download data: TXT

(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) Sinorhizobium meliloti lives as a soil saprophyte, and engages in a nitrogen fixing symbiosis with plant roots. To succeed in such diverse environments, the bacteria must continually adjust gene expression. Transcriptional plasticity in eubacteria is often mediated by alternative sigma factors interacting with core RNA polymerase. The S. meliloti genome encodes 14 of these alternative sigmas, including 11 extracytoplasmic function (ECF) sigmas. more...

Organism:

Medicago truncatula; Sinorhizobium meliloti

Type:

Expression profiling by array

Platform:

GPL9757

6 Samples

Download data: CEL

(Submitter supplied) Background- The plant growth promoting rhizobacterium Paenibacillus riograndensis SBR5 is a promising candidate to serve as crop inoculant. Despite its potential regarding environmental and economic benefits, the species P. riograndensis is poorly characterized. Here, we performed for the first time a detailed transcriptome analysis of P. riograndensis SBR5 using RNAseq technology. Results- Sequence analysis of the library enriched in 5’-ends of the primary transcripts was used to identify 1,082 TSS belonging to novel transcripts and allowed us to determine a promoter consensus sequence and regulatory sequences in 5’ untranslated regions including riboswitches Conclusions- Our RNAseq analysis provides insight into the P. more...

Organism:

Paenibacillus riograndensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23461

2 Samples

Download data: XLS

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

Organism:

Klebsiella pneumoniae subsp. pneumoniae MGH 78578; Klebsiella pneumoniae; Escherichia coli K-12

Type:

Expression profiling by array; Expression profiling by high throughput sequencing; Other

Platforms:

GPL15233 GPL15223 GPL15232

6 Samples

Download data: PAIR

(Submitter supplied) We report the application of single-molecule-based sequencing technology for high-throughput profiling of transcription start sites for two enterobacteria: Escherichia coli and Klebsiella pneumoniae.By obtaining over fourteen billion bases of sequence from 5' RACE (rapid amplification of cDNA ends) followed by deep sequencing, we generated genome-wide TSS (transcription start site) maps for those two species. more...

Organism:

Klebsiella pneumoniae; Escherichia coli K-12

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL15232 GPL15233

4 Samples

Download data: TXT

(Submitter supplied) Investigation of whole genome gene expression level in Klebsiella pneumoniae MGH78578 grown up to mid-exponential phase in M9 minimal media supplemented with 0.2% glucose

Organism:

Klebsiella pneumoniae subsp. pneumoniae MGH 78578

Type:

Expression profiling by array

Platform:

GPL15223

2 Samples

Download data: PAIR

(Submitter supplied) Prochlorococcus is a genus of abundant and ecologically important marine cyanobacteria. Here, we present the comprehensive comparison of the structure and composition of the transcriptomes of two closely related Prochlorococcus strains, which, despite their similarities, have adapted their gene pool to specific environmental constraints. We used large-scale strand-specific cDNA sequencing, microarray RNA profiling and computational analyses to characterize the transcriptomes of Prochlorococcus sp. more...

Organism:

Prochlorococcus marinus subsp. pastoris str. CCMP1986; Prochlorococcus phage P-SSM4; Prochlorococcus marinus str. MIT 9313; Tiamatvirus PSSP7

Type:

Expression profiling by array

Platform:

GPL8853

5 Samples

Download data: CEL, TXT

(Submitter supplied) We report an applicaton of small RNA sequencing using high throughput next generation sequencing to identify the small RNA content of cell lines. By sequencing over 30 million reads we could identify a new class of small RNAs previousy observed with tiling arrays and mapping to promoter regions of coding genes. We also identified a large number of small RNAs corresponding to internal exons of coding genes. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9115

40 Samples

Download data: TXT

(Submitter supplied) The obligate intracellular human pathogen Chlamydia pneumoniae was subjected to dRNA-Seq to gain insights into the transcriptome. The two distinct life cycle forms elementary bodies (EB) and reticulate bodies (RB) were isolated from human Hep2 cell line by differential gradient centrifugation.

Organism:

Chlamydia pneumoniae CWL029

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11140

8 Samples

Download data: TXT

(Submitter supplied) We prepared and sequenced Start-seq libraries from rat (Rattus norgevicus) primary neural progenitor cells. Over 48 million uniquely mappable reads from two independent biological replicates allowed us to define the TSSs of 7,365 known genes in the rn6 genome, reannotating 2,503 TSSs by more than 5 base pairs, characterize promoter-associated antisense transcription, and profile Pol II pausing. By combining TSS data with polyA-selected RNA sequencing, we also identified thousands of potential new genes producing stable RNA as well as non-genic transcripts representing possible regulatory elements. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18694

6 Samples

Download data: BW, TSV

(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) Listeria monocytogenes is a human, food-borne pathogen. Genomic comparisons between L. monocytogenes and Listeria innocua, a closely related non-pathogenic species, were pivotal in the identification of protein coding genes essential for virulence. However, no comprehensive comparison has focused on the non-coding genome. We used strand-specific cDNA sequencing to produce genome-wide transcription start site (TSS) maps for both organisms, and developed a publicly available integrative browser to visualize and analyze both transcriptomes in different growth conditions and genetic backgrounds. more...

Organism:

Listeria innocua Clip11262; Listeria monocytogenes EGD-e

Type:

Other

Platforms:

GPL15272 GPL15273

16 Samples

Download data: TXT

(Submitter supplied) A strong promoter increases transcription of the genes of interest and enhances the production of various valuable substances. For a hyperthermophilic archaeon Thermococcus onnurineus NA1, which can produce H2 by carbon monoxide oxidation, we searched for a novel endogenous strong promoter by transcriptome analysis using high-throughput RNA sequencing. Based on the relative transcript abundance, we selected one promoter to encode a hypothetical gene, of which homologs were found only in several Thermococcales strains. more...

Organism:

Thermococcus onnurineus NA1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19533

2 Samples

Download data: TXT

(Submitter supplied) The model cyanobacterium Synechocystis sp. PCC 6803 was used for a systematic survey of differential expression with a focus on antisense (as)RNAs and non-coding (nc)RNAs. A microarray was constucted with on average 5 probes for each transcript known thus far, including ncRNAs and asRNAs. The resulting 20,431 individual probes are duplicated on the array (Agilent 4x44k custom array) representing a technical replicate. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by array; Non-coding RNA profiling by array

Dataset:

GDS3744

Platform:

GPL8567

12 Samples

Download data: TXT

(Submitter supplied) The model cyanobacterium Synechocystis sp. PCC 6803 was used for a systematic survey on the number and types of antisense (as)RNAs. A tiled microarray was constructed with probes for both strands of the genes or intergenic spacers with candidate transcripts predicted by an algorithm and an equally sized and distributed control set. The resulting 102,739 individual probes cover an accumulated length of 1,441,146 nt or about 40% of the total chromosome sequence of Synechocystis 6803. more...

Organism:

Synechocystis sp. PCC 6803

Type:

Expression profiling by genome tiling array; Non-coding RNA profiling by genome tiling array

Platform:

GPL8071

4 Samples

Download data: TXT