GEO DataSets

(Submitter supplied) WT, ∆rhlB and ∆rppH strains were globally profiled for mRNA half-lives using rifampicin treatment followed by RNA-seq. Wild type(WT) was compared to ∆rhlB (deleted RNA helicase RhlB gene) and ∆rppH (deleted RppH gene) strains

Organism:

Caulobacter vibrioides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32153

24 Samples

Download data: TXT

(Submitter supplied) PNPase, one of the major enzymes with 3ʹ-to-5ʹ single-stranded RNA (ssRNA) degradation and processing activities, can interact with the RNA helicase RhlB independent of RNA degradosome formation in E. coli. Here we report that loss of interaction between RhlB and PNPase impacts cysteine homeostasis in E. coli. By random mutagenesis, we identified a mutant RhlBP238L that loses 75% of its ability to interact with PNPase, but retains normal interaction with RNase E and RNA in addition to exhibiting normal helicase activity. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL18708

6 Samples

Download data: GPR

(Submitter supplied) Comparison of Bacillus subtilis wild type and cshA mutant at exponential versus stationary phase. Detailed description (other than provided below) of growth conditions, RNA preparation, cDNA synthesis and hybridization conditions can be found in the submitted paper.

Organism:

Bacillus subtilis

Type:

Expression profiling by array

Platform:

GPL6031

4 Samples

Download data: TXT

(Submitter supplied) Purpose: We wanted to determine the transcriptome profile of PAO1 wild type, PAO1ΔrhlE1, PAO1ΔrhlE2 and PAO1ΔrhlE1ΔrhlE2 mutants on swarming conditions. Method: Cells were harvested using the RNA bacteria protect solution (QIAGEN). Total RNAs was extracted and purified using Monarch RNA isolation kit (NEB), treated with DNase I (Promega) three times to remove contaminating genomic DNA and re-purified again using phenol-chloroform. more...

Organism:

Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18782

8 Samples

Download data: FASTA, TXT

(Submitter supplied) Abstract: RNase E, an essential endoribonuclease of Escherichia coli, interacts through its C-terminal region with multiple other proteins to form a complex termed the RNA degradosome. To investigate the degradosome's proposed role as an RNA decay machine, we used DNA microarrays to globally assess alterations in the steady-state abundance and decay of 4,289 E. coli mRNAs at single-gene resolution in bacteria carrying mutations in the degradosome constituents RNase E, polynucleotide phosphorylase, RhlB helicase, and enolase. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL2821

78 Samples

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(Submitter supplied) mRNA decay in E. Coli degradosome mutants and their parental strains following transcriptional arrest with rifampicin. Abstract: RNase E, an essential endoribonuclease of Escherichia coli, interacts through its C-terminal region with multiple other proteins to form a complex termed the RNA degradosome. To investigate the degradosome's proposed role as an RNA decay machine, we used DNA microarrays to globally assess alterations in the steady-state abundance and decay of 4,289 E. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL2821

61 Samples

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(Submitter supplied) Comparative transcript abundance in E. Coli degradosome mutants and their parental strains. Abstract: RNase E, an essential endoribonuclease of Escherichia coli, interacts through its C-terminal region with multiple other proteins to form a complex termed the RNA degradosome. To investigate the degradosome's proposed role as an RNA decay machine, we used DNA microarrays to globally assess alterations in the steady-state abundance and decay of 4,289 E. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL2821

17 Samples

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(Submitter supplied) We report that TOG1 coordinates global changes of gene expression upon high temperature to support rice thermotolerant growth. We performed gene ontology (GO) enrichment analysis of the differentially expressed genes in rice seedlings grown at 25 ℃ and 30 ℃ and found that when temperature increases, wild-type dramatically adjusts the expression level of hundreds of genes in GO terms polysaccharide metabolic process, carbohydrate metabolic process, glucan metabolic process, carbon fixation, response to stimulus and organic substance metabolic process required for growth. more...

Organism:

Oryza sativa Indica Group

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14553

4 Samples

Download data: TXT

(Submitter supplied) We performed mRNA-seq on mouse embryonic stem cells, with four DEAD-box family proteins, DDX10, DDX24, DDX27, DDX54 being partially depleted using RNA interference. Knockdown of EGFP was carried out as a control. By comparing all four knockdowns, we observed misregulation of a highly-overlapping set of genes, indicating that they regulate mRNA levels through a shared pathway.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23479

15 Samples

Download data: TXT