GEO DataSets

(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) 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) 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:

Acinetobacter baumannii; Staphylococcus aureus; Klebsiella aerogenes; Staphylococcus epidermidis

Type:

Expression profiling by high throughput sequencing; Other

4 related Platforms

30 Samples

Download data: TSV

(Submitter supplied) Background: The human pathogen Corynebacterium diphtheriae is the causative agent of the disease diphtheria. In the 1990s a large diphtheria outbreak in Eastern Europe was caused by the strain C. diphtheriae NCTC 13129. Although the genome was sequenced several years ago, not much is known about the transcriptome. Our aim was to use RNA Sequencing to close this knowledge gap and gain insights into the transcriptional landscape of C. more...

Organism:

Corynebacterium diphtheriae NCTC 13129

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23376

7 Samples

Download data: XLSX

(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:

Mycoplasmoides pneumoniae M129

Type:

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

Platforms:

GPL7821 GPL7822

295 Samples

Download data: GPR

(Submitter supplied) Two main articles have used this data. The small bacterium Mycoplasma pneumoniae with its annotated 689 protein-coding genes and 44 RNAs constitutes an ideal system for global and conditional transcription analysis in bacteria. We have combined spotted arrays under more than 120 conditions with several strand-specific, high resolution tiling arrays to obtain an unprecedented level of detail of bacterial gene expression. more...

Organism:

Mycoplasmoides pneumoniae M129

Type:

Expression profiling by array

Platform:

GPL7822

252 Samples

Download data: GPR

(Submitter supplied) Two main articles have used this data. The small bacterium Mycoplasma pneumoniae with its annotated 689 protein-coding genes and 44 RNAs constitutes an ideal system for global and conditional transcription analysis in bacteria. We have combined spotted arrays under more than 120 conditions with several strand-specific, high resolution tiling arrays to obtain an unprecedented level of detail of bacterial gene expression. more...

Organism:

Mycoplasmoides pneumoniae M129

Type:

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

Platform:

GPL7821

43 Samples

Download data

(Submitter supplied) We used the RNA-seq technology to do a genome-wide transcriptional analysis of A. pleuropneumoniae strain JL03 and investigated the transcriptome structure at a single-nucleotide resolution.The RNA-Seq based transcriptome map validated annotated genes and corrected annotations of open reading frames in the genome, and led to the identification of many functional elements (e.g. regions encoding novel proteins, non-coding sRNAs and operon structures).

Organism:

Actinobacillus pleuropneumoniae serovar 3 str. JL03

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20603

1 Sample

Download data: BED

(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) In this study transcriptional start sites (TSS) of E. coli were determined for several growth conditions

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17024 GPL15010

22 Samples

Download data: WIG

(Submitter supplied) The objective of the study is to obtain a high resolution transcription map of S. pneumoniae genome and make it available through a genome browser. The study also help to identify gene expression pattern, presence of small RNAs, Antisense expression and operon structure.

Organism:

Streptococcus pneumoniae

Type:

Expression profiling by genome tiling array

Platform:

GPL7177

2 Samples

Download data: PAIR

(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) 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) Campylobacter jejuni is currently the leading cause of bacterial gastroenteritis in humans. Comparison of multiple Campylobacter strains revealed a high genetic and phenotypic diversity. However, little is known about differences in transcriptome organization, gene expression, and small RNA (sRNA) repertoires. Here we present the first comparative primary transcriptome analysis based on the differential RNA–seq (dRNA–seq) of four C. more...

Organism:

Campylobacter jejuni RM1221; Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819; Campylobacter jejuni subsp. jejuni 81-176; Campylobacter jejuni subsp. jejuni 81116

Type:

Expression profiling by high throughput sequencing

4 related Platforms

16 Samples

Download data: WIG

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

Organism:

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

Type:

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

Platforms:

GPL15233 GPL15232 GPL15223

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) A whole genome tiling microarray based on the published sequence of the Anaplasma phagocytophilum (Ap) strain Hz genome was used to measure transcriptional activity of Ap grown to late stage in three cell lines representing the diversity of host cells naturally infected by Ap: two human cell lines, HL-60 (promyelocytic leukocyte) and HMEC-1 (microvascular endothelial), and the tick (Ixodes scapularis) cell line ISE6. more...

Organism:

Anaplasma phagocytophilum str. HZ; Ixodes scapularis; Homo sapiens

Type:

Expression profiling by genome tiling array

Platform:

GPL6869

18 Samples

Download data: CEL, TXT

(Submitter supplied) Previous molecular and mechanistic studies have identified several principles of prokaryotic transcription, but less is known about the global transcriptional architecture of bacterial genomes. Here we perform a comprehensive study of a cyanobacterial transcriptome, that of Synechococcus elongatus PCC 7942, generated by combining three high-resolution data sets: RNA sequencing, tiling expression microarrays, and RNA polymerase chromatin immunoprecipitation (ChIP) sequencing. more...

Organism:

Synechococcus elongatus PCC 7942 = FACHB-805

Type:

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

Platforms:

GPL13530 GPL13535

13 Samples

Download data: GPR, TXT, WIG