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Series GSE100024 Query DataSets for GSE100024
Status Public on Mar 05, 2018
Title RNA-seq analysis of glucose fermentation by the natural Isopropanol producer Clostridium beijerinckii DSM6423
Organism Clostridium beijerinckii
Experiment type Expression profiling by high throughput sequencing
Summary 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.
Methods : A RNA-Seq approach was chosen in order to have a timelapse study of DSM 6423 throughout the fermentation process. Three independent duplicate fermentations of DSM 6423 were carried out in bioreactors on three different weeks, showing good reproducibility. On each cultivation, five biomass samples were collected for RNA-Seq analyses.and DNA was eliminated after DNAse I treatment (AM1906, Invitrogen). The 15 resulting RNA samples were sequenced and analyzed using the previously reconstructed genome of DSM 6423.
Results: Using a data analysis workflow (TAMARA) developed by the Genoscope platform of Evry, we were able to highlight the transcriptional regulation along the fermentation by calculating the transcription profiles of each gene, using the 3h sample as reference. Clustering was performed using CAST algorithm revealed 8 clusters containing 953 genes and corresponding to genes up-regulated at 6, 8, 11 or 24 hours and gene down-regulated at 6, 8, 11 or 24 hours.
Conclusion : Such analyses were carried out in this study and provide useful data to better understand the genetic background and the physiological specificities of C. beijerinckii DSM6423 isopropanol producer. Notably, this work is the first omic study of a natural IBE producer. The data gathered needs time for proper exploitation, but a better understanding of the metabolic pathways and various genes involved opens the door for future targeted approaches.
 
Overall design Comparative analysis of samples taken from a serie a fermentations performed in controled conditions
 
Contributor(s) de Gérando HM, Bidard-Michelot F, Jourdier E, López-Contreras AM, Ferreira NL
Citation(s) 29636009, 30578270
Submission date Jun 14, 2017
Last update date Jul 25, 2021
Contact name Frederique Bidard
E-mail(s) frederique.bidard-michelot@ifpen.fr
Organization name IFPEN
Department Biotechnology
Street address 1-4 avenue de Bois Préau
City Rueil Malmaison
ZIP/Postal code 92852
Country France
 
Platforms (1)
GPL23579 Illumina NextSeq 500 (Clostridium beijerinckii)
Samples (15)
GSM2668033 Fermentor N°1 Sample 3h (D1)
GSM2668034 Fermentor N°1 Sample 6h (D2)
GSM2668035 Fermentor N°1 Sample 8h (D3)
Relations
BioProject PRJNA390516
SRA SRP109175

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE100024_RAW.tar 2.4 Mb (http)(custom) TAR (of CSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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