GEO DataSets

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

Organism:

Shewanella sp. W3-18-1; Shewanella sp. MR-4; Shewanella sp. MR-7; Shewanella sp. ANA-3; Shewanella oneidensis MR-1; Shewanella loihica PV-4; Shewanella amazonensis SB2B; 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) 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) 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) 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 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) 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) To investigate the architecture of the E. coli K-12 transcriptome, we used two RNA-Seq technologies to analyze strand-specific transcription at single-nucleotide resolution. We analyzed the data by using an organizational schema to annotate the promoters and terminators that define transcription units across the genome. Our results showed that most (ca. two-thirds) operons have a single promoter and terminator, whereas one-third of operons contain multiple transcription units. more...

Organism:

Escherichia coli K-12

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17884

26 Samples

Download data: TXT, WIG

(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) Bacterial promoters consist of core sequence motifs termed –35 and –10 boxes. The consensus motifs are TTGACA and TATAAT, respectively, which were identified from leading investigations on E. coli. However, the consensus sequences are not likely to fit genetically divergent bacteria. The sigma factor of the genus Bifidobacterium has a characteristic polar domain in the N-terminus, suggesting the possibility of specific promoter recognition. more...

Organism:

Bifidobacterium longum NCC2705

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27983

3 Samples

Download data: XLSX