GEO DataSets

(Submitter supplied) Purpose: A goal of this study was to identify genes induced in the mother cell during Clostridium difficile sporulation (specifically in a σE-, σK-, and SpoIIID-dependent manner). Methods: Whole genome RNA sequencing was performed on wildtype, sigE-, sigK- and spoIIID- C. difficile strains (strain 630 background; JIR8094 = parent strain), and the transcriptional profiles of the different mutants during growth on 70:30 agar plates were determined using an Illumina MiSeq1000. more...

Organism:

Clostridioides difficile 630

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19481

12 Samples

Download data: TXT

(Submitter supplied) Compartment-specific control of gene expression during Bacillus subtilis sporulation is governed by a cascade of four sigma factors, sigmaF and sigmaG in the forespore and sigmaE and sigmaK in the mother cell. In this work, we combined transcriptional analyses and transcriptional start site mapping to define the sigmaF, sigmaE, sigmaG and sigmaK regulons in Clostridium difficile. A total of about 225 genes were under the control of these sigma factors: 25 in the sigmaF regulon, 97 sigmaE-dependent genes, 50 sigmaG-governed genes and 56 genes specifically controlled by sigmaK. more...

Organism:

Clostridioides difficile

Type:

Expression profiling by array

Platform:

GPL10556

2 Samples

Download data: GPR, TXT, XLS

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

Organism:

Clostridioides difficile

Type:

Expression profiling by array

Platform:

GPL10556

18 Samples

Download data: GPR

(Submitter supplied) Compartment-specific control of gene expression during Bacillus subtilis sporulation is governed by a cascade of four sigma factors, sigmaF and sigmaG in the forespore and sigmaE and sigmaK in the mother cell. In this work, we combined transcriptional analyses and transcriptional start site mapping to define the sigmaF, sigmaE, sigmaG and sigmaK regulons in Clostridium difficile. A total of about 225 genes were under the control of these sigma factors: 25 in the sigmaF regulon, 97 sigmaE-dependent genes, 50 sigmaG-governed genes and 56 genes specifically controlled by sigmaK. more...

Organism:

Clostridioides difficile

Type:

Expression profiling by array

Platform:

GPL10556

4 Samples

Download data: GPR, TXT, XLS

(Submitter supplied) Compartment-specific control of gene expression during Bacillus subtilis sporulation is governed by a cascade of four sigma factors, sigmaF and sigmaG in the forespore and sigmaE and sigmaK in the mother cell. In this work, we combined transcriptional analyses and transcriptional start site mapping to define the sigmaF, sigmaE, sigmaG and sigmaK regulons in Clostridium difficile. A total of about 225 genes were under the control of these sigma factors: 25 in the sigmaF regulon, 97 sigmaE-dependent genes, 50 sigmaG-governed genes and 56 genes specifically controlled by sigmaK. more...

Organism:

Clostridioides difficile

Type:

Expression profiling by array

Platform:

GPL10556

4 Samples

Download data: GPR, TXT, XLS

(Submitter supplied) Compartment-specific control of gene expression during Bacillus subtilis sporulation is governed by a cascade of four sigma factors, sigmaF and sigmaG in the forespore and sigmaE and sigmaK in the mother cell. In this work, we combined transcriptional analyses and transcriptional start site mapping to define the sigmaF, sigmaE, sigmaG and sigmaK regulons in Clostridium difficile. A total of about 225 genes were under the control of these sigma factors: 25 in the sigmaF regulon, 97 sigmaE-dependent genes, 50 sigmaG-governed genes and 56 genes specifically controlled by sigmaK. more...

Organism:

Clostridioides difficile

Type:

Expression profiling by array

Platform:

GPL10556

4 Samples

Download data: GPR, TXT, XLS

(Submitter supplied) Compartment-specific control of gene expression during Bacillus subtilis sporulation is governed by a cascade of four sigma factors, sigmaF and sigmaG in the forespore and sigmaE and sigmaK in the mother cell. In this work, we combined transcriptional analyses and transcriptional start site mapping to define the sigmaF, sigmaE, sigmaG and sigmaK regulons in Clostridium difficile. A total of about 225 genes were under the control of these sigma factors: 25 in the sigmaF regulon, 97 sigmaE-dependent genes, 50 sigmaG-governed genes and 56 genes specifically controlled by sigmaK. more...

Organism:

Clostridioides difficile

Type:

Expression profiling by array

Platform:

GPL10556

4 Samples

Download data: GPR, TXT, XLS

(Submitter supplied) Purpose: The goal of this study was to identify genes whose expression is induced during sporulation in a Spo0A-, σF-, σE-, σG-, and σK-dependent manner. Methods: Whole genome RNA sequencing was performed on wildtype, spo0A-, sigF-, sigE-, sigG-, and sigK- C. difficile strains (strain 630 background; JIR8094 = parent strain), and the transcriptional profiles of the different mutants during growth on 70:30 agar plates were determined using an Illumina HiSeq1000. more...

Organism:

Clostridioides difficile 630

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18533

18 Samples

Download data: TXT

(Submitter supplied) This series of experiments was designed to identify the program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis. The mother cell is one of two cell types generated by asymmetric division of sporulating cells approximately two hours after initiation of sporulation. The program is governed by a hierarchical cascade consisting of the transcription factors: sigmaE, sigmaK, GerE, GerR (YlbO) and SpoIIID. more...

Organism:

Bacillus subtilis

Type:

Expression profiling by array

Platform:

GPL1353

15 Samples

Download data: TIFF

(Submitter supplied) Clostridium acetobutylicum, the endospore-forming anaerobe best known for its ABE (acetone-butanol-ethanol) fermentation, has received renewed attention recently for the biological production of butanol, both for bulk chemical production and as a potential biofuel. With butanol production in mind, most of the recent research on C. acetobutylicum has focused on increasing butanol production, tolerance to butanol, and optimizing it for various substrates. more...

Organism:

Clostridium acetobutylicum ATCC 824

Type:

Expression profiling by array

Platform:

GPL10908

24 Samples

Download data: TXT

(Submitter supplied) Genes encoding the alternative sigma factor SigmaB, involved in the general stress response in firmicutes, as well as its regulators are present in the genome of the enteropathogen Clostridium difficile. We inactivated the sigB gene using the ClosTron technology in order to identify the role of this sigma factor in the physiology of this bacterium. Transcriptomic experiments showed that SigB positively and negatively controlls several genes involved in different cellular processes such as metabolism, sporulation and stress response.

Organism:

Clostridioides difficile

Type:

Expression profiling by array

Platform:

GPL18319

4 Samples

Download data: GPR, TXT, XLS

(Submitter supplied) Clostridium difficile is an important nosocomial pathogen and the leading cause of hospital-acquired diarrhea. Antibiotic use is the primary risk factor for the development of C. difficile-associated disease because it disrupts normal protective gut flora and enables C. difficile to colonize the colon. C. difficile damages host tissue by secreting toxins and disseminates by forming spores. The toxin-encoding genes, tcdA and tcdB are part of a pathogenicity locus, which also encodes the gene tcdR that codes for the toxin genes positive regulator. more...

Organism:

Clostridioides difficile

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22304

4 Samples

Download data: XLS

(Submitter supplied) RNAseq and LC/MS metabolomics analysis of C. difficile strain 630 grown in BHIS media with 50% (vol/vol) faecal water added, compared with control BHIS containing only the additional PBS used for prep of Faecal water. Cells grown in biological triplicates to late log phase (T=6h) prior to harvest. Goal was to determine changes in gene expression caused by exposure to Faecal water, and changes in the metabolite profile of faecal water containing medium when incubated with actively growing C. more...

Organism:

Clostridioides difficile 630

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24774

6 Samples

Download data: TXT

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

Organism:

Clostridioides difficile

Type:

Expression profiling by array

Platforms:

GPL10556 GPL18319

8 Samples

Download data: GPR

(Submitter supplied) Transcriptional profiling of C. difficile 630E strain vs. an Hfq antisense after 7.5h of growth inTYt.

Organism:

Clostridioides difficile

Type:

Expression profiling by array

Platform:

GPL18319

4 Samples

Download data: GPR, TXT, XLS

(Submitter supplied) Clostridium difficile is an emergent human pathogen and the most common cause of nosocomial diarrhea. Our recent deep-sequencing data strongly suggest the importance of RNA-based mechanisms for the control of gene expression in C. difficile. The RNA chaperon protein Hfq is a key component of post-transcriptional regulatory network in various bacterial systems. In an effort to understand the function of Hfq in C. more...

Organism:

Clostridioides difficile

Type:

Expression profiling by array

Platform:

GPL10556

4 Samples

Download data: GPR, TXT, XLS

(Submitter supplied) Using our newly designed C. acetobutylicum arrays we analyzed the mRNA changes during a time course experiment (up to 66 h) paying special attention on the study of the late timepoints. Keywords: time course

Organism:

Clostridium acetobutylicum ATCC 824; Clostridium acetobutylicum

Type:

Expression profiling by array

Platform:

GPL4412

56 Samples

Download data: TXT

(Submitter supplied) C. acetobutylicum ATCC824 Transcriptional array v2 includes over 20K 60-mer oligonucleotide probes selected after experimental testing of our proof-of-concept platforms GPL4029 and GPL4030. The programs Comm_Oligo (Li, He et al. 2005), ROSO (Reymond, Charles et al. 2004), YODA (Nordberg 2005), ArrayOligoSelector (Bozdech, Zhu et al. 2003), OligoWiz 2.0 (Wernersson and Nielsen 2005) and Picky (Chou, Hsia et al. more...

Organism:

Clostridium acetobutylicum ATCC 824

2 Series

68 Samples

Download data

(Submitter supplied) Transcriptional profiling of C. difficile 630E strain vs. a sig54 mutant after 6h of growth in TY.

Organism:

Clostridioides difficile

Type:

Expression profiling by array

Platform:

GPL10556

4 Samples

Download data: GPR, TXT, XLS

(Submitter supplied) The transcriptome analysis by microarray was applied on wild-type and degenerated strains of C. beijerinckii NCIMB8052 (WT-8052 and DG-8052, respectively) to elucidate its mechanism of degeneration during solvent fermentation. The comparison of gene expression pattern in relation to ABE production is expected to provide insights toward metabolically engineering of C. beijerinckii NCIMB8052 with prevention of degeneration and eventually enhancement of ABE production.

Organism:

Clostridium beijerinckii NCIMB 8052

Type:

Expression profiling by array

Platform:

GPL19469

6 Samples

Download data: TXT