Transcriptomics

Dataset Information

2

Transcriptomics comparison and transcriptional architecture improvement of Clostridium thermocellum ATCC27405 using systems biology data and bioinformatics approaches


ABSTRACT: Background: Clostridium thermocellum is a Gram-positive, anaerobic, thermophilic bacterium with a great potential to be a consolidated bioprocessing biocatalyst that can ferment cellulose to ethanol. To understand its physiology and genetic targets for future strain development, we have carried out several studies including ethanol-tolerant mutant resequencing and ethanol shock experiments. Methods: In this study, several approaches were applied to enrich mRNA for next-generation sequencing based RNA-Seq and the transcriptomic profiling of C. thermocellum ethanol shock responses was investigated using high-density tiling array and RNA-Seq. Correlations among different transcriptomic platforms of expression array, tiling array, and RNA-Seq were then compared, and data generated from systems biology studies were used for transcriptional architecture improvement. Results: Our results indicate that cloning-based Sanger sequencing can be used for mRNA enrichment ratio determination, and low-copy number plasmid performed better than high-copy one for cDNA library construction. In addition, high correlations were observed among same array platform using different analyses as well as those between two different array platforms of tiling and expression array when probe intensity was compared. Correlations between RNA-Seq and array results especially the one between RNA-Seq and tiling array are also high. Moreover, combining both RNA-Seq and microarray data the transcriptional architecture of C. thermocellum including the prediction and verification of novel transcript (gene), transcriptional start site (TSS), CAZyme genes, ncRNA, and operon were systematically updated and improved. Conclusions: RNA-seq has high correlation with array-based transcriptomic platforms and can provide additional information for transcriptional architecture and genome annotation improvement, which will facilitate future omics-based studies. A twelve array study using total RNA recovered from wild-type cultures of Clostridium thermocellum at different time points of 30, 60, and 120 min post-inoculation with 3.95 g/L [0.5% (v/v)] treatment compred to that of control without ethanol supplementation. Two biological replicates for treatment and control condition.

ORGANISM(S): Hungateiclostridium thermocellum ATCC 27405  

SUBMITTER: Shihui YANG   Martin Keller  Shihui Yang  Miguel Rodriguez Jr  Robert L Hettich  Zamin Yang  Timothy J Tschaplinski  Richard J Giannone  Dice Lezlee  Steven D Brown  Nancy L Engle 

PROVIDER: E-GEOD-26889 | ArrayExpress | 2015-11-08

SECONDARY ACCESSION(S): GSE26889PRJNA135951

REPOSITORIES: GEO, ArrayExpress

Similar Datasets

| GSE26889 | GEO
2014-05-08 | E-GEOD-26926 | ArrayExpress
2012-08-16 | E-GEOD-25236 | ArrayExpress
2013-05-16 | E-GEOD-47010 | ArrayExpress
2013-01-01 | E-GEOD-40402 | ArrayExpress
2014-01-15 | E-GEOD-54082 | ArrayExpress
| GSE26926 | GEO
2015-07-29 | E-GEOD-71465 | ArrayExpress
2012-08-16 | GSE25236 | GEO
2013-09-04 | E-GEOD-21165 | ArrayExpress