Comment[ArrayExpressAccession]	E-GEOD-52495
MAGE-TAB Version	1.1					
Public Release Date	2013-11-20
Investigation Title	Genome and transcriptome of Clostridium phytofermentans catalyst for the direct conversion of plant feedstocks to fuels					
Comment[Submitted Name]	Genome and transcriptome of Clostridium phytofermentans catalyst for the direct conversion of plant feedstocks to fuels
Experiment Description	Clostridium phytofermentans was recently isolated from forest soil and is distinguished by its capacity to directly ferment plant cell wall polysaccharides into ethanol as the primary product, suggesting that it possesses unusual catabolic pathways.  The objective of the present study was to understand the molecular mechanisms of biomass conversion to ethanol in a single organism, Clostridium phytofermentans, by analyzing its complete genome and transcriptome during growth on plant carbohydrates.  The saccharolytic versatility of C. phytofermentans is reflected in a diversity of genes encoding ATP-binding cassette sugar transporters and glycoside hydrolases, many of which may have been acquired through horizontal gene transfer.  These genes are frequently organized as operons that may be controlled individually by the many transcriptional regulators identified in the genome.  Preferential ethanol production may be due to high levels of expression of multiple ethanol dehydrogenases and additional pathways maximizing ethanol yield.  The genome also encodes three different proteinaceous bacterial microcompartments with the capacity to compartmentalize pathways that divert fermentation intermediates to various products.  These characteristics make C. phytofermentans an attractive resource for improving the efficiency and speed of biomass conversion to biofuels. C. phytofermentans was cultured anaerobically on different carbohydrates sources to determine carbohydrates specific expression patterns.  The data in this series consists two independent RNA preparations from replicate cultures.					
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl				
Person Last Name	Blanchard	Petit	Hayes	Blanchard		
Person First Name	Jeffrey	Elsa	James	Jeffrey		
Person Mid Initials	L					
Person Email	jeffb@bio.umass.edu					
Person Affiliation	University of Massachusetts Amherst					
Person Phone	413-577-2130					
Person Address	Biology, University of Massachusetts Amherst, 203 Morrill Science Center IVN, Amherst, MA, USA					
Person Roles	submitter					
Protocol Name	P-GSE52495-1	P-GSE52495-4	P-GSE52495-5	P-GSE52495-2	P-GSE52495-3	P-GSE52495-6
Protocol Description	The resulting raw spot image data files were processed into pivot and quality report files using Microarray Suite version 5.0.   Expression values were calculated using the Custom Array Analysis Software (CAAS) package (http://www.sourceforge.net/projects/caas-microarray/) that implements the Robust Multichip Average method.  The quality of the microarray datasets were analyzed using probe-level modeling procedures provided by the affyPLM package in BioConductor.  No image artifacts due to array manufacturing or processing were observed.  In summary, all quality control checks indicated that the RNA purification, cDNA synthesis, labeling and hybridization procedures adapted for use in C. phytofermentans resulted in high quality data. ID_REF =  VALUE = RMA expression values	Ten M-NM-<g total RNA from each sample was used as template to synthesize labeled cDNAs using Affymetrix GeneChip DNA Labeling Reagent Kits.	The labeled cDNA samples were hybridized on the arrays according to Affymetrix guidelines.	C. phytofermentans ISDg was cultured in anaerobic medium GS-2CB [20]. Growth on single carbon-source utilized anaerobic medium derived from GS-2CB and containing the following (g l-1): yeast extract, 6.0; urea, 2.1; KH2PO4, 4.0; Na2HPO4, 6.5; trisodium citrate dihydrate, 3.0; L-cysteine hydrochloride monohydrate, 2.0; resazurin, 1; with pH adjusted to 7.0 using KOH. This medium was supplemented with 0.3% (wt/vol) of the specific substrate added as a filter-sterilized solution to the sterile medium. Broth cultures were incubated at 30M-KM-^ZC under anaerobic conditions (100% N2) as described in by Hungate [30]. Growth was determined spectrophotometrically by monitoring changes in optical density at 660 nm. RNA was purified from mid-exponential phase cultures.	RNA was isolated from two replicates of each type of culture at mid exponential phase. Briefly, cells were flash-frozen by immersion in liquid nitrogen, harvested by centrifugation for 5 min at 8,000 rpm at 4M-0C and re-suspended in 100 M-5l in TE buffer pH 8 (EMD Chemicals) containing 2 mg/ml lysozyme (Sigma-Aldrich) and incubated at 37M-0C for 40 min. Total RNA was isolated using the RNeasy RNA purification kit (QIAGEN) according to the manufacturerM-bM-^@M-^Ys instructions. Contaminating DNA in total RNA preparations was removed with RNase-free DNase I (QIAGEN).	The hybridized arrays were scanned with a GeneChip Scanner 3000.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	CARBOHYDRATE SOURCE					
Experimental Factor Type	carbohydrate source					
Comment[SecondaryAccession]	GSE52495					
Comment[GEOReleaseDate]	2013-11-20					
Comment[ArrayExpressSubmissionDate]	2013-11-19					
Comment[GEOLastUpdateDate]	2013-11-21					
Comment[AEExperimentType]	transcription profiling by array					
SDRF File	E-GEOD-52495.sdrf.txt