GEO DataSets

(Submitter supplied) We developed Methyl-SNP-seq, a technology that takes advantage of the redundancy of the double helix, to extract the methylation and sequence information from a single original DNA molecule We demonstrate the usefulness of this technology on a broad spectrum of applications ranging from allele specific methylation analysis in humans to methylation identification in complex bacterial communities.

Organism:

Clostridium acetobutylicum; Escherichia coli; Homo sapiens

Type:

Other

4 related Platforms

9 Samples

Download data: COV, VCF

(Submitter supplied) Arthrobacter sp. CGMCC 3584 are able to produce high yields of extracellular cyclic adenosine monophosphate (cAMP), which plays a vital role in the field of treatment of disease and animal food, during aerobic fermentation. Comparative transcriptomic analysis revealed that arpde inactivation had two major effects on metabolism: inhibition of glycolysis, PP pathway, and amino acid metabolism; promotion of the purine metabolism and carbon flux from the precursor PRPP, which benefited cAMP production.

Organism:

Arthrobacter sp. CGMCC 3584; Clostridium acetobutylicum; Arthrobacter sp.

Type:

Expression profiling by array

Platform:

GPL19013

8 Samples

Download data: TXT

(Submitter supplied) To identify the putative genes under the regulation of two component system BtrK/BtrR, we performed a comparative transcriptomic analysis of the BtrK/BtrR overexpressing strain and the contron strain. Finally, we found that BtrK/BtrR was a global regulator and exerted pleiotropic regulatory role in C. acetobutylicum

Organism:

Clostridium acetobutylicum

Type:

Expression profiling by array

Platform:

GPL27577

8 Samples

Download data: TXT

(Submitter supplied) In this study, we studied the fibrolytic potential of the rumen microbiota in the rumen of 6 lambs separated from their dams from 12h of age and artificially fed with milk replacer (MR) and starter feed from d8, in absence (3 lambs) or presence (3 lambs) of a combination of the live yeast Saccharomyces cerevisiae CNCM I-1077 and selected yeast metabolites. The fibrolytic potential of the rumen microbiota of the lambs at 56 days of age was analyzed with a DNA microarray (FibroChip) targeting genes coding for 8 glycoside hydrolase (GH) families.

Organism:

Butyrivibrio fibrisolvens; Ruminococcus flavefaciens; Piromyces communis; Pseudobacteroides cellulosolvens; Eudiplodinium maggii; Segatella bryantii; Acetivibrio clariflavus; uncultured Neocallimastigales; Bacteroides fragilis; Xylanibacter ruminicola; Ruminococcus albus; Enterococcus faecium; Clostridium acetobutylicum; Acetivibrio thermocellus; Clostridium beijerinckii; Levilactobacillus brevis; Microbiota; Bacteroides ovatus; Fibrobacter intestinalis; Bacteroides sp.; Epidinium caudatum; Polyplastron multivesiculatum; Butyrivibrio hungatei; Epidinium ecaudatum; Bacteroides xylanisolvens; Cellulosilyticum ruminicola; Ruminococcus champanellensis; Orpinomyces sp.; Bacteroides thetaiotaomicron; Fibrobacter succinogenes; Clostridium cellulovorans; Bifidobacterium adolescentis; Cellulomonas fimi; Neocallimastix frontalis; [Eubacterium] cellulosolvens; Lachnospira eligens; Ruminococcus sp.; Piromyces sp.; Roseburia intestinalis; Roseburia hominis; Selenomonas ruminantium; Lactococcus lactis; Clostridioides difficile; Ruminiclostridium cellulolyticum; Limosilactobacillus fermentum; Cellulomonas flavigena; Neocallimastix patriciarum; Bifidobacterium animalis; Agathobacter rectalis; Enterobacter sp.; Orpinomyces joyonii; Piromyces rhizinflatus; Piromyces sp. 'equi'; Pseudobutyrivibrio xylanivorans; Bifidobacterium longum

Type:

Genome variation profiling by array

Platform:

GPL25777

6 Samples

Download data: TXT

(Submitter supplied) Background: Bacterial fermentation of carbohydrates from sustainable lignocellulosic biomass into biofuels by the anaerobic bacterium Clostridium acetobutylicum is a promising alternative energy source to fossil fuels. Understanding the complex metabolic pathways it employs and how they are regulated will contribute to improved biofuel production. Recently, it has been demonstrated that xylose is not appreciably fermented in the presence of arabinose, suggesting a hierarchy of pentose utilization in this organism. more...

Organism:

Clostridium acetobutylicum ATCC 824

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24347

48 Samples

Download data: CSV

(Submitter supplied) Ruminants are the most efficient herbivorous animals to transform plant biomass into edible products, principally thanks to the rumen microbiota that produces a large array of enzymes responsible for the hydrolysis of plant cell wall polysaccharides. Several biotic and abiotic factors influence the efficiency of fiber degradation, which can ultimately impact the animal productivity and health. To provide more insight on mechanisms involved in the modulation of fibrolytic activity, a functional DNA microarray targeting genes coding for key enzymes involved in cellulose and hemicellulose degradation by rumen microbiota was designed. more...

Organism:

Ruminococcus flavefaciens; Limosilactobacillus fermentum; Piromyces communis; Pseudobacteroides cellulosolvens; Eudiplodinium maggii; Fibrobacter succinogenes subsp. succinogenes S85; Segatella bryantii; Acetivibrio clariflavus; Bacteroides fragilis; Ruminococcus albus; Enterococcus faecium; Acetivibrio thermocellus; Clostridium beijerinckii; Levilactobacillus brevis; Fibrobacter intestinalis; Epidinium caudatum; Polyplastron multivesiculatum; Orpinomyces joyonii; Piromyces rhizinflatus; Piromyces sp. 'equi'; Epidinium ecaudatum; Bacteroides xylanisolvens; Cellulosilyticum ruminicola; Ruminococcus champanellensis; Bacteroides thetaiotaomicron; Fibrobacter succinogenes; Xylanibacter ruminicola; Clostridium acetobutylicum; Clostridium cellulovorans; Bifidobacterium adolescentis; Cellulomonas fimi; Neocallimastix frontalis; Bacteroides ovatus; [Eubacterium] cellulosolvens; Bacteroides sp.; Lachnospira eligens; Ruminococcus sp.; Piromyces sp.; Roseburia intestinalis; Butyrivibrio hungatei; Roseburia hominis; bovine gut metagenome; Bacteroides xylanisolvens XB1A; Orpinomyces sp.; Butyrivibrio fibrisolvens; Selenomonas ruminantium; Lactococcus lactis; Clostridioides difficile; Ruminiclostridium cellulolyticum; Cellulomonas flavigena; Neocallimastix patriciarum; Bifidobacterium animalis; Agathobacter rectalis; Enterobacter sp.; Escherichia coli K-12; Pseudobutyrivibrio xylanivorans; Bifidobacterium longum; uncultured Neocallimastigales

Type:

Expression profiling by array; Other

Platform:

GPL24327

14 Samples

Download data: TXT

(Submitter supplied) Arthrobacter sp. CGMCC 3584 are able to produce high yields of extracellular cyclic adenosine monophosphate (cAMP), which plays a vital role in the field of treatment of disease and animal food, during aerobic fermentation. DNA array-based transcriptional analysis of Arthrobacter cells was conducted to elucidate the higher productivity of cAMP under high oxygen supply. Results showed that 14.1% and 19.3% of the whole genome genes were up-regulated and down-regulated notably, respectively. more...

Organism:

Arthrobacter sp. CGMCC 3584; Clostridium acetobutylicum; Arthrobacter sp.

Type:

Expression profiling by array

Platform:

GPL19013

8 Samples

Download data: TXT

(Submitter supplied) Transcriptomic analysis was applied to acidogenic, solventogenic and alcohologenic steady-state C. acetobutylicum cells for understanding the regulation of the metabolism of this organism. Used microarray is Clostridium acetobutylicum ATCC824 transcriptional 44k v4, correspondance to GPL10908

Organism:

Clostridium acetobutylicum ATCC 824

Type:

Expression profiling by array

Platform:

GPL10908

9 Samples

Download data: TXT

(Submitter supplied) Previously, we performed DNA array-based transcriptomic analysis of Clostridium acetobutylicum biofilm adsorbed onto fibrous matrix in batch fermentation. Here, to further shed light on the transcriptomic modulation of maturing Clostridium acetobutylicum biofilm, we performed the DNA array-based transcriptomic analysis in repeated-batch fermentation. Significant time course changes in expression levels were observed for the genes involved in amino acid metabolism, oligopeptide ABC transporter, nitrogen fixation, and various other processes.

Organism:

Clostridium acetobutylicum DSM 1731; Clostridium acetobutylicum; Arthrobacter sp.

Type:

Expression profiling by array

Platform:

GPL19020

8 Samples

Download data: TXT

(Submitter supplied) Transcriptomic analysis was applied to acidogenic, solventogenic and alcohologenic steady-state C. acetobutylicum cells for understanding the regulation of the metabolism of this organism. Used microarray is Clostridium acetobutylicum ATCC824 transcriptional 44k v4, correspondance to GPL10908

Organism:

Clostridium acetobutylicum ATCC 824

Type:

Expression profiling by array

Platform:

GPL10908

36 Samples

Download data: TXT

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

Organism:

Clostridium acetobutylicum; Arthrobacter sp.; Clostridium acetobutylicum DSM 1731

Type:

Expression profiling by array

Platforms:

GPL19020 GPL19013

16 Samples

Download data: TXT

(Submitter supplied) Immobilization of Clostridium acetobutylicum B3 onto fibrous matrix by surface-adsorption was developed and applied to biobutanol production. The immobilized C. acetobutylicum B3 cells formed biofilm and showed dramatically improved butanol tolerance and production rate. DNA array-based transcriptional analysis of C.acetobutylicum B3 biofilm cells was conducted to elucidate the gene expression profile of the biofilm cells. more...

Organism:

Clostridium acetobutylicum; Arthrobacter sp.; Clostridium acetobutylicum DSM 1731

Type:

Expression profiling by array

Platform:

GPL19020

8 Samples

Download data: TXT

(Submitter supplied) Immobilization of Clostridium acetobutylicum B3 onto fibrous matrix by surface-adsorption was developed and applied to biobutanol production. The immobilized C. acetobutylicum B3 cells formed biofilm and showed dramatically improved butanol tolerance and production rate. DNA array-based transcriptional analysis of C.acetobutylicum B3 biofilm cells was conducted to elucidate the gene expression profile of the biofilm cells. more...

Organism:

Clostridium acetobutylicum; Arthrobacter sp.

Type:

Expression profiling by array

Platform:

GPL19013

8 Samples

Download data: TXT

(Submitter supplied) The transcription profile of C. acetobutylicum to two major metabolite stress, butanol and butyric acid, was comprehensively investigated at three different concentrations of each metabolite and at four different time points (15, 30, 60 and 75 min post stress). All experiments were performed in 3 parallel biological replicates and the RNA extraction was perfomed in a manner to retain the small RNAs and hence, investigate their role and expression under stress.

Organism:

Clostridium acetobutylicum

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17364

84 Samples

Download data: TXT

(Submitter supplied) Clostridium acetobutylicum is a Gram positive, endospore forming firmicute that has been known as the model organims for ABE (acetone-butanol-ethanol) fermentation. With its ability to consume a wide variety of substrates, C. acetobutylicum carries out a biphasic ABE fermentation, which consists of the acidogenic growth phase with the formation of butyric acid and acetic acid, followed by the solventogenic stationary phase with the formation of acetone, butanol and ethanol, characterised by the reassimilation of acids. more...

Organism:

Clostridium acetobutylicum ATCC 824

Type:

Expression profiling by array

Platform:

GPL10908

24 Samples

Download data: TXT

(Submitter supplied) Clostridium acetobutylicum is a Gram positive, endospore forming firmicute that has been known as the model organims for ABE (acetone-butanol-ethanol) fermentation. With its ability to consume a wide variety of substrates, C. acetobutylicum carries out a biphasic ABE fermentation, which consists of the acidogenic growth phase with the formation of butyric acid and acetic acid, followed by the solventogenic stationary phase with the formation of acetone, butanol and ethanol, characterised by the reassimilation of acids. more...

Organism:

Clostridium acetobutylicum ATCC 824

Type:

Expression profiling by array

Platform:

GPL10908

24 Samples

Download data: TXT

(Submitter supplied) Clostridium acetobutylicum is a typical bacterium of major importance to industrial butanol production. In order to dissect the regulatory network pertaining to the industrial application of this bacterium, catabolite control protein A (CcpA) was investigated for its global function by DNA microarray.It showed that CcpA of C. acetobutylicum controls hundreds of genes, not only carbon metabolism, but also solvent production and sporulation in the life cycle.The results here demonstrated that CcpA is an important pleiotropic regulator related to some specific physiological and biochemical process in butanol-producing C. more...

Organism:

Clostridium acetobutylicum

Type:

Expression profiling by array

Platform:

GPL14821

8 Samples

Download data: TXT

(Submitter supplied) Transcriptomic profiling of gene expression in EA 2018 relative to that of ATCC824 revealed several key genes related to solvent formation. For example, spo0A and adhEII have higher expression level, and most of the acid formation related genes have lower expression level in EA 2018.

Organism:

Clostridium acetobutylicum; Clostridium acetobutylicum EA 2018; Clostridium acetobutylicum ATCC 824

Type:

Expression profiling by array

Platform:

GPL10678

12 Samples

Download data: TXT

(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) Investigation of whole genome gene expression levels in Clostridium acetobutylicum strain 824 grown individually on starch, galactose, lactose, mannose, fructose, glucose, arabinose, xylose, cellobiose, maltose, sucrose

Organism:

Clostridium acetobutylicum ATCC 824

Type:

Expression profiling by array

Platform:

GPL9387

33 Samples

Download data: PAIR