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Series GSE47010 Query DataSets for GSE47010
Status Public on May 16, 2013
Title Clostridium thermocellum ATCC27405 Transcriptomic Profiles during growth on Populus and switchgrass
Platform organism Acetivibrio thermocellus ATCC 27405
Sample organism Acetivibrio thermocellus 27405
Experiment type Expression profiling by array
Summary 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. High quality RNA was extracted using a method we report for C. thermocellum grown on solid substrates. Transcriptome profiles were obtained at two time points during actively growing fermentations (12 h and 37 h post inoculation). A comparison of two transcriptomic analytical techniques, microarray and RNAseq, was performed and the data analyzed for statistical significance. When thresholds for genes passing significance of FDR>0.05 were applied, microarray (2351 genes) had a greater number of significant genes relative to RNA-seq (280 genes when normalized by KDMM). When a 2-fold difference in expression threshold was applied, seventy-three genes were significantly differentially expressed in common between the two techniques. We identified genes differentially expressed when C. thermocellum ATC 27405 was grown on the two biomass substrates, with two putative efflux/transport systems highly differentially regulated (>5-fold). This study has revealed consistency between these two transcriptomics analytical platforms that gives confidence in our switch from the DNA microarray platform to an RNAseq based platform for routine transcriptomics analyses.
 
Overall design 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. High quality RNA was extracted using a method we report for C. thermocellum grown on solid substrates. Transcriptome profiles were obtained at two time points during actively growing fermentations (12 h and 37 h post inoculation). A comparison of two transcriptomic analytical techniques, microarray and RNAseq, was performed and the data analyzed for statistical significance.
 
Contributor(s) Brown SD, Wilson CM, Johnson CM, Klingeman DM, Rodriguez M Jr
Citation(s) 24295562
Submission date May 16, 2013
Last update date Jul 10, 2018
Contact name Dawn Marie Klingeman
E-mail(s) klingemandm@ornl.gov
Phone +18655763435
Organization name Oak Ridge National Lab
Department Biosciences Division
Lab RNA Profiling
Street address 1 Bethel Valley Rd building 15056 Rm 366 MS 6038
City Oak Ridge
State/province TN
ZIP/Postal code 37831-6342
Country USA
 
Platforms (1)
GPL17171 Clostridium thermocellum ATCC 27405 HX12 array (3 x 720k array) [080724_C_thermo_27405_expr]
Samples (8)
GSM1142896 F185_Pop_12 hr rep1
GSM1142897 F185_Pop_37 hr rep1
GSM1142898 F186_Swg_12 hr_rep1
Relations
BioProject PRJNA203267

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

Supplementary file Size Download File type/resource
GSE47010_RAW.tar 25.4 Mb (http)(custom) TAR (of CALLS, PAIR)
Processed data included within Sample table
Processed data provided as supplementary file

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