Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-Seq of Clostridium cellulovorans cultured in different carbon sources in exponential phase

ABSTRACT: When Clostridium cellulovorans cultured in different carbon sources respectively, with pH controlled at 7.0 in the fed-batch fermentation, the main product was butyrate. In order to understand the carbon and energy flux of Clostridium cellulovorans, comparative transcriptome in exponential phase was performed.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Clostridium cellulovorans

SUBMITTER: Dandan Jiang

PROVIDER: E-MTAB-12360 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Energy conservation and carbon flux arrangement in the fermentation of Clostridium ljungdahlii with CO or CO2/H2

Project description:Clostridium ljungdahlii not only utilizes CO, but also H2 as energy source during autotrophic growth. In theory, CO is a more energetically and thermodynamically favourable energy source than H2 in the gas fermentation of C. ljungdahlii. However, how C. ljungdahlii conserves energy for growth and ethanol/acetate formation grown on CO or CO2/H2 is not in great detail. In this study, C. ljungdahlii was fermented on CO and CO2/ H2 at pH 6.0 with 0.1 MPa gas pressure. C. ljungdahlii produced 27 g/L acetate, 9 g/L ethanol, 8 g/L 2,3-butanediol and traces of lactate in the presence of CO as energy source, while it produced 25.8  0.1 g/L acetate, 1.8  0.1 g/L ethanol, 0.7  0.01g/L 2,3-butanediol and trances of lactate in the same fermentation condition using H2 as energy source. Therefore, comparative transcriptomes between cells grown on CO and cells grown on H2/CO2 were performed to investigate gene expression profiles based on three biological replicates.

2020-04-01 | E-MTAB-8260 | biostudies-arrayexpress

RNA-Seq of Clostridium ljungdahlii with CO as the sources of carbon and energy in exponetial phase against stationary phase

Project description:More than 5 g/L ethanol was detected at 84 h in the late-exponential phase with 0.1 MPa at pH 6.0 in the batch fermentation of C. ljungdahlii grown autotrophically. Interestingly, ethanol started to be reassimilated in the stationary phase. In order to understand the metabolic flux of ethanol, comparative transcriptome between exponential and stationary phases were performed.

2022-07-26 | E-MTAB-7753 | biostudies-arrayexpress

2 Role of aldehyde dehydrogenase on the metabolic regulation in Clostridium ljungdahlii fermentation

Project description:Clostridium ljungdahlii can utilize CO as energy source during autotrophic growth. C. ljungdahlii grows sufficiently in CO and produces ethanol as the main product. In this study, C. ljungdahlii wild type and mutant were fermented on CO. C. ljungdahlii produced more ethanol than the ΔadhE1 mutant. The results showed that aldehyde dehydrogenase inactivation led to inefficient metabolism in C. ljungdahlii. Thus, comparative transcriptomes among cells grown on CO of WT and ΔadhE1 mutant were performed to investigate gene expression profiles based on three biological replicates.

2023-06-27 | E-MTAB-13021 | biostudies-arrayexpress

Role of aldehyde dehydrogenase on the metabolic regulation in Clostridium ljungdahlii fermentation

Project description:Clostridium ljungdahlii not only utilizes CO, but also H2 as energy source during autotrophic growth. And C. ljungdahlii also grows in fructose fermentation. In theory, fructose is a more energetically favourable energy source than syngas in the fermentation of C. ljungdahlii. However, C. ljungdahlii grows insufficiently in fructose and produces less acetate and ethanol, compared to syngas fermentation. In this study, C. ljungdahlii wild type and mutants were fermented on fructose. C. ljungdahlii produced less ethanol than the ΔadhE1 mutant and consumed less fructose. The ΔadhE1+2 mutant cannot grow in the syngas fermentation and produced less ethanol among the three strains. The results showed that aldehyde dehydrogenase inactivation led to efficient metabolism in C. ljungdahlii and the bifunctional aldehyde/alcohol dehydrogenases inactivation led to decrease metabolism. Thus, comparative transcriptomes among cells grown on fructose of three strains were performed to investigate gene expression profiles based on three biological replicates.

2023-06-27 | E-MTAB-13020 | biostudies-arrayexpress

Enhanced solvent titer in the fermentation of Clostridium beijerinckii through application of metabolic controls

Project description:Clostridium beijerinckii is an anaerobic strain and well known for acetone-ethanol-butanol (ABE) fermentation using carbohydrates derived from cellulose or starch. During ABE fermentation, various byproducts are formed, mainly including acids (acetate, butyrate and lactate) and gas (hydrogen and carbon dioxide). recently, we found that Clostridium beijerinckii is able to produce a new product that had never been reported before and tightly regulated by pH and nitrogen source.

2021-12-02 | E-MTAB-11154 | biostudies-arrayexpress

miRNA microarray analysis to explore the expression profiles of miRNAs using the same liver tissues of NFD-fed mice and HFD-fed mice

Project description:The miRNA microarray analysis was performed to explore the expression profiles of miRNAs using the same liver tissues of NFD-fed mice and HFD-fed mice  Summary: An abstract of the experiment and the data analysis.  Project Description: Sample and experiment information.  Array Information: miRCURY™ LNA expression array information.  Data Analysis for miRNAs: 1. Low intensity filtering and data normalization: After low intensity miRNAs filtering, raw signal intensities are normalized in Median method. (miRNAs that intensities>=30 in all samples are chosen for calculating normalization factor) 2. Quality assessment of miRNA data after filtering: Contains box plot, Correlation Matrix and scatter plot for miRNAs after normalization. 3. Differentially expressed miRNAs screening: Contains significant differentially expressed miRNAs that pass Volcano Plot filtering. (Fold Change>=1.5, P-value<=0.05) 4. Heat map and hierarchical clustering: Hierarchical clustering on the significant differentially expressed miRNAs that passed Volcano Plots filtering.  Sample RNA Quality Control: Sample quality control data file from Nanodrop 1000 spectrophotometer and standard denaturing agarose gel electrophoresis.  Methods: A brief introduction for microarray, experiment, and data analysis.  FAQ: Frequently asked question Additional miRNA Array Analysis (charge an extra fee):  Prediction Analysis for Microarrays (PAM analysis)  miRNA Target Gene Prediction and Functional Analysis Additional files provided:  Graphs (*.jpg)  Raw Intensity File(*.xls, raw miRNAs signal intensity)  Layout File (*.gal, the files contain information on the positioning of the capture probes on the array and microRNA annotations for your species of interest)  Raw data files produced by GenePix Pro 6.0

2022-11-23 | E-MTAB-8731 | biostudies-arrayexpress

Gene expression in CD8+ T cells derived from Nrdp1+/+ and Nrdp1-/- mice

Project description:The purpose of this study was to determine which genes are differentially regulated by the E3 ligase Nrdp1 in CD8+ T cells after treatments with anti-CD3/CD28 Abs. The results demonstrate increased induction of cytotoxicity-associated genes in Nrdp1-/- mice than in Nrdp1+/+ mice after activation. Thus Nrdp1 may be involved in the regulation of TCR signaling. Naive CD8+ T cells derived spleens of Nrdp1+/+ and Nrdp1-/- mice were either untreated or treated with immobilized anti-CD3 (5 μg/ml) and soluble anti-CD28 (1 μg/ml) Abs for 4h or 8h. Equal amounts of RNA were assayed for gene expression using Affymetrix mouse 430 2.0 arrays.

2015-08-03 | E-GEOD-70393 | biostudies-arrayexpress

Transcription profiling by array of the effect of SAH on brain cells in white matter region of mice

Project description:Using the SAH model to conduct experiments, set 5 groups of experimental groups and 5 groups of control groups. Studying the effects on the white matter cells of normal mice and the mice with SAH

2019-10-10 | E-MTAB-8407 | biostudies-arrayexpress

Expression analysis of effect of Intestine-specific knockdown of KLF5 on radiation induced intestinal injury

Project description:The objective was to determine the role of Krüppel-like factor 5 (KLF5) in radiation-induced intestinal injury. Mice with intestinal-specific knockdown of KLF5 (Cre+ mice) were generated and their response to radiation was compared with controls (Cre- mice). Mice were given 15 Gy total body irradiation (TBI). The mice intestines were harvested at 6h post TBI and screened for differentially expressed genes by microarray analysis. We identified 11,004 and 2,466 differentially expressed genes in non-irradiated and irradiated mice at 6h post TBI, respectively. KLF5 knockdown down-regulated genes related to DNA damage repair pathways such as nucleotide excision repair, mismatch repair, non-homologous end joining and the Fanconi anemia pathway, which may suggest a novel function of KLF5. A four chip study using total RNA recovered from four pooled intestine tissues of four experimental groups. The four experimental groups respectively were the 6h-cre+ group, 6h-cre- group, con-cre+ group and con-cre- group. Equal mass amounts of total RNA were pooled from each small intestine to yield a sample representing RNA from 3 separate mice in each group. One pooled sample in every group were tested with one chip. Each chip measures the expression level of 44,170 genes from C57BL/6 mouse (background) with three 60-mer probe pairs per gene.

2015-03-10 | E-GEOD-66655 | biostudies-arrayexpress

RNA and cell free miRNA in one family of Kallmann's syndrome

Project description:Kallmann Syndrome (KS) is a rare human genetic disorder characterized by the hypogonadotropic hypogonadism with the reduction or absence of olfactory sense. The mutations on the multiple genes including Chemokine Prokineticin-2 (PROK2) were considered to contribute to the abnormal migration of gonadotropin-releasing hormone (GnRH) neurons in embryonic stage. Here, we submit RNA-seq of the peripheral blood and the cell free miRNA-seq in the serum of one family, in which the KS patient has the same mutation of PROK2 (c.223-4C>A) with his mother, and the genetic phenotype of his father is normal. The sexual development and function of his parents are normal.

2020-05-01 | E-MTAB-8919 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data