Comment[ArrayExpressAccession]	E-GEOD-54825
MAGE-TAB Version	1.1		
Public Release Date	2015-04-10
Investigation Title	Transcriptional reprogramming of engineered cellobiose-utilizing Saccharomyces cerevisiae in response to cellobiose revealed by RNA-Seq		
Comment[Submitted Name]	Transcriptional reprogramming of engineered cellobiose-utilizing Saccharomyces cerevisiae in response to cellobiose revealed by RNA-Seq
Experiment Description	Saccharomyces cerevisiae cannot metabolize cellobiose in nature. Here, S. cerevisiae was engineered to achieve cellobiose utilization by introducing both a cellodextrin transporter gene (cdt-1) and an intracellular β-glucosidase gene (gh1-1) from Neurospora crassa. We sequenced mRNA from anaerobic exponential cultures of engineered S. cerevisiae grown on cellobiose or glucose as a single carbon source in biological triplicate. Differences in gene expression between cellobiose and glucose metabolism revealed by RNA deep sequencing indicated that cellobiose metabolism induced mitochondrial activation and reduced amino acid biosynthesis under fermentation conditions. mRNA levels in cellobiose-grown and glucose-grown cells of engineered cellobiose-utilizing Saccharomyces cerevisiae were examined by deep sequencing, in triplicate, using Illumina Genome Analyzer-II. We sequenced 3 samples from cellobiose-grown cells and 3 samples from glucose-grown cells and identified differential expressions in the cellobiose versus glucose fermentations by using mRNA levels of glucose-grown cells as a reference.		
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	Cate	Lin	Cate
Person First Name	Jamie	Yuping	Jamie
Person Mid Initials	H. D.		H
Person Email	jcate@lbl.gov		
Person Affiliation	University of California, Berkeley		
Person Address	Departments of Chemistry and MCB, Energy Biosciences Institute, University of California, Berkeley, Stanley Hall 708B, Berkeley, CA, USA		
Person Roles	submitter		
Protocol Name	P-GSE54825-2	P-GSE54825-1	
Protocol Description	Illumina Casava_v1.8.0 software used for basecalling. Sequenced reads were trimmed for adaptor sequence. Sequence reads were assembled and analyzed in CLC Genomics Workbench 6.5 (CLC Bio, Aarhus, Denmark). The Saccharomyces cerevisiae S288C genome was downloaded from RefSeq at the NCBI (http://www.ncbi.nlm.nih.gov/refseq/) including 16 chromosomes and the mitochondrial genome. The genes for N. crassa b-glucosidase gh1-1 and EGFP-tagged N. crassa cellodextrin transporter cdt-1 were manually annotated and combined with the S. cerevisiae S288C genome as the reference (total size of 12.17 Mb). Expression values were normalized by calculating the reads per kilobase of mRNA exon per million mapped reads (RPKM), and further normalized using the option of “By totals”. To identify differential expression in the cellobiose versus glucose fermentations, an unpaired two-group comparison was used to generate fold-changes and further analyzed for statistical significance by using Baggerley’s test. Genome_build: R64-1-1 Supplementary_files_format_and_content: Excel file include RPKM values for all the samples and differential expressions in the cellobiose versus glucose fermentations including fold change and FDR p-values.	Total RNA was extracted using the RiboPure Yeast kit (Ambion, Austin, TX, USA), according to manufacturer's instructions, except cells were disrupted by bead-beating 3 times for 30 sec, with a 30 sec pause between runs. 4 µg of total RNA were used to prepare the multiplexing libraries with barcodes following the standard instructions of the Illumina TruSeq RNA Sample Prep Kit.	
Protocol Type	normalization data transformation protocol	nucleic acid library construction protocol	
Experimental Factor Name	carbon source		
Experimental Factor Type	carbon source		
Publication Title	Leveraging transcription factors to speed cellobiose fermentation by Saccharomyces cerevisiae.		
Publication Author List	Lin Y, Chomvong K, Acosta-Sampson L, Estrela R, Galazka JM, Kim SR, Jin YS, Cate JH		
PubMed ID	25435910		
Publication DOI	10.1186/s13068-014-0126-6		
Comment[SecondaryAccession]	GSE54825		
Comment[GEOReleaseDate]	2015-04-10		
Comment[ArrayExpressSubmissionDate]	2014-02-10		
Comment[GEOLastUpdateDate]	2015-05-31		
Comment[AEExperimentType]	RNA-seq of coding RNA		
Comment[AdditionalFile:Data1]	GSE54825_Cellobiose_versus_Glucose.xlsx		
Comment[SecondaryAccession]	SRP037533		
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR1166442-SRR1166447		
SDRF File	E-GEOD-54825.sdrf.txt