GEO DataSets

(Submitter supplied) The thermophilic anaerobe Clostridium thermocellum is a candidate consolidated bioprocessing (CBP) biocatalyst for cellulosic ethanol production. It expresses enzymes for both cellulose solubilization and its fermentation to produce lignocellulosic ethanol. To gain insights into the C. thermocellum genes, using an updated version of the C. thermocellum ATCC 27405 genome annotation, that are required for specific growth on the cellulosic feedstocks of either pretreated switchgrass or Populus, duplicate fermentations were conducted with a 5 g/L solid substrate loading. more...

Organism:

Acetivibrio thermocellus ATCC 27405; Acetivibrio thermocellus 27405

Type:

Expression profiling by array

Platform:

GPL17171

8 Samples

Download data: CALLS, PAIR

(Submitter supplied) Background: The thermophilic anaerobe Clostridium thermocellum is a candidate consolidated bioprocessing (CBP) biocatalyst for cellulosic ethanol production. It is capable of both cellulose solubilization and its fermentation to produce lignocellulosic ethanol. Intolerance to stresses routinely encountered during industrial fermentations may hinder the commercial development of this organism. Results: In this study, C. more...

Organism:

Acetivibrio thermocellus ATCC 27405

Type:

Expression profiling by array

Platform:

GPL15992

43 Samples

Download data: TXT

(Submitter supplied) Clostridium thermocellum is a candidate for cellulosic ethanol production. It expresses enzymes for both cellulose solubilization and its fermentation to produce lignocellulosic ethanol. Understanding how this organism regulates gene expression is of importance for developing a better fundamental understanding of this industrial relevant bacterium. We are primarily interested in gene regulation by three predicted LacI regulators. more...

Organism:

Acetivibrio thermocellus DSM 1313

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20122

36 Samples

Download data: TXT

(Submitter supplied) Background: The ability of Clostridium thermocellum ATCC 27405 wild-type strain to hydrolyze cellulose and ferment the degradation products directly to ethanol and other metabolic byproducts makes it an attractive candidate for consolidated bioprocessing of cellulosic biomass to biofuels. In this study, whole-genome microarrays were used to investigate the expression of C. thermocellum mRNA during growth on crystalline cellulose in controlled replicate batch fermentations. more...

Organism:

Acetivibrio thermocellus ATCC 27405

Type:

Expression profiling by array

Platform:

GPL13640

39 Samples

Download data: TXT

(Submitter supplied) Clostridium thermocellum is a Gram-positive, anaerobic, thermophilic bacterium that ferments cellulose into ethanol. It is a candidate industrial consolidated bioprocess (CBP) biocatalyst for lignocellulosic bioethanol production. However, C. thermocellum is relatively sensitive to ethanol compared to yeast. Previous studies have investigated the membrane and protein composition of wild-type and ethanol tolerant strains, but relatively little is known about the genome changes associated with the ethanol tolerant C. more...

Organism:

Acetivibrio thermocellus ATCC 27405

Type:

Expression profiling by array

Platform:

GPL11186

30 Samples

Download data: CALLS, PAIR

(Submitter supplied) Clostridium thermocellum is a promising CBP candidate organism capable of directly converting lignocellulosic biomass to ethanol. Low yields, productivities and growth inhibition prevent industrial deployment of this organism for commodity fuel production. Symptoms of potential redox imbalance such as incomplete substrate utilization, and fermentation products characteristic of overflow metabolism, have been observed during growth. more...

Organism:

Acetivibrio thermocellus ATCC 27405; Acetivibrio thermocellus DSM 1313

Type:

Expression profiling by array

Platform:

GPL20749

32 Samples

Download data: TXT

(Submitter supplied) DNA sequences for the 3163 C. thermocellum ATCC 27405 predicted protein-encoding genes were obtained from The Joint Genome Institute using sequence assembled in November 2003. Oligonucleotide probes that represented the whole genome of C. thermocellum were designed using the CommOligo software and were commercially synthesized without modification (MWG Biotech, High Point, NC) in 96-well plates. The concentration of the probes was adjusted to 100 pmol/JlL, transferred to 384-well printing plates in a final concentration of 50% dimethyl sulfoxide using a BioMek FX liquid handling robot (Beckman-Coulter, Fullerton, CA) and then spotted onto UltraGAPS glass slides (Corning Life Sciences, Corning, NY) using a BioRobotics Microgrid II microarrayer (Genomic Solutions, Ann Arbor, MI) in a dust-free clean room maintained at 21°C and 50% relative humidity. more...

Organism:

Acetivibrio thermocellus ATCC 27405

1 Series

39 Samples

Download data: TXT

(Submitter supplied) RNA-seq analysis revealed that genes involved in urea uptake and metabolism were significantly upregulated in the Clo1313_2031 deletion strain, suggesting that deletion of Clo1313_2031 mimics nitrogen starvation in C. thermocellum. Additionally, genes encoding the RNF-complex were also more highly expressed and in turn may have a potential role in increasing ethanol production.

Organism:

Acetivibrio thermocellus DSM 1313

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20122

8 Samples

Download data: TXT, XLSX

(Submitter supplied) Earlier studies pointed to the ability of C. thermocellum to exquisitely control gene expression in response to growth rate and the presence of insoluble cellulose or soluble compounds such as cellobiose. This microarray study was carried out in order to examine expression responses of the entire genome. The use of the chemostat technique allowed the effects of different growth rates to be analyzed separately from the effects of different substrates.

Organism:

Acetivibrio thermocellus ATCC 27405

Type:

Expression profiling by array

Platform:

GPL10557

11 Samples

Download data: PAIR

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28038

30 Samples

Download data

(Submitter supplied) Purpose: Recombinant human erythropoietin administration studies involving “omics” approaches have demonstrated a gene-expression signature that could aid detection of blood doping. However, current anti-doping testing does not involve blood collection into tubes with RNA preservative. This study investigated if whole blood in short-term storage could be used for transcriptomic analysis despite lacking RNA preservation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28038

16 Samples

Download data: TXT

(Submitter supplied) Purpose: Recombinant human erythropoietin administration studies involving “omics” approaches have demonstrated a gene-expression signature that could aid detection of blood doping. However, current anti-doping testing does not involve blood collection into tubes with RNA preservative. This study investigated if whole blood in long-term storage could be used for transcriptomic analysis despite lacking RNA preservation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28038

14 Samples

Download data: TXT

(Submitter supplied) Recombinant human erythropoietin administration studies involving transcriptomic approaches have demonstrated a gene-expression signature that could aid detection of blood doping. However, current anti-doping testing does not involve blood collection into tubes with RNA preservative. This study investigated if whole blood in long-term storage and whole blood leftover from standard haematological testing in short-term storage could be used for transcriptomic analysis despite lacking RNA preservative. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

32 Samples

Download data: CEL, CHP

(Submitter supplied) Differential RNA-Seq analyses to investigate the basis for metabolic inhibition of Clostridium thermocellum M1570 by xylose. The M1570 strain was developed in the C. thermocellum DSM 1313 Δhpt background strain. Lactate dehydrogenase (Ldh) and phosphotransacetylase (Pta) genes are deleted (Argyros DA, Tripathi SA, Barrett TF, Rogers SR, Feinberg LF, Olson DG, Foden JM, Miller BB, Lynd LR, Hogsett DA, Caiazza NC: High ethanol titers from cellulose by using metabolically engineered thermophilic, anaerobic microbes. more...

Organism:

Acetivibrio thermocellus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21122

8 Samples

Download data: TXT, XLSX

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL570 GPL11154

18 Samples

Download data: CEL, TXT

(Submitter supplied) The RNA samples from HT-29 (ATCC) colon cancer cell line were reverse transcribed to build cDNA libraries and categorized into 3 groups with different concentrations of 5-aza-deoxy-cytidine (5-Aza); in each group three replicative 150 mm cultures were treated with: 1) dimethyl sulfoxide (vehicle alone, 0 μM 5-Aza); 2) 5μM 5-Aza and 3) 10 μM 5-Aza; for five days. This experiment was also performed parallel on a commercial Affymetrix microarray [GSE41364] and the aim of the study was to compare the two platforms on gene expression measurements and differentially expressed gene (DEG) detection. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

9 Samples

Download data: TXT

(Submitter supplied) The RNA samples from HT-29 (ATCC) colon cancer cell line were reverse transcribed into cDNAs and categorized in 3 groups with different concentrations of 5-aza-deoxy-cytidine (5-Aza); in each group three replicative 150 mm cultures were treated with: 1) dimethyl sulfoxide (vehicle alone, 0 μM 5-Aza); 2) 5μM 5-Aza and 3) 10 μM 5-Aza; for five days We then used Affymetrix microarray platform to profile the gene expression of the 3 HT29 cell groups (3 replicates in each group) in order to search for differentially expressed genes

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

9 Samples

Download data: CEL

(Submitter supplied) Purpose:C. beijerinckii DSM 6423 is the most cited natural IpOH producer. Improving the natural production of this strain through a targeted approach required a full sequencing and characterization of its genome, together with transcriptomic analyses of its own regulations.The goals of this study are then to evaluate the transcriptional profile (RNA-Seq) of C. beijerinckii DSM6423, a natural isopropanol producer, during a fermentation of glucose in controlled bioreactors. more...

Organism:

Clostridium beijerinckii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23579

15 Samples

Download data: CSV

(Submitter supplied) The high cellulose digestion capability of the anaerobic thermophilic bacterium, Clostridium thermocellum, can be attributed to its efficient glycoside hydrolase system, consisting of both a free-enzyme system and a cellulosomal system, wherein carbohydrate active enzymes (CAZymes) are organized by primary and secondary scaffoldin proteins into large protein complexes bound to the bacterial cell wall. more...

Organism:

Acetivibrio thermocellus ATCC 27405; Acetivibrio thermocellus DSM 1313

Type:

Expression profiling by array

Platform:

GPL18170

14 Samples

Download data: TXT