GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1324496 Query DataSets for GSM1324496
Status Public on Apr 10, 2015
Title JCYL001B
Sample type SRA
Source name Glucose-grown cells
Organism Saccharomyces cerevisiae
Characteristics strain: Engineered BY4742 containing cellobiose-utilizing pathway
growth condition: Anaerobic
carbon source: Glucose
Extracted molecule total RNA
Extraction protocol 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.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
Data processing 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 ( 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.
Submission date Feb 10, 2014
Last update date May 15, 2019
Contact name Yuping Lin
Organization name Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences
Street address 32 West 7th Avenue, Tianjin Airport Economic Area
City Tianjin
State/province Tianjin
ZIP/Postal code 300308
Country China
Platform ID GPL9377
Series (1)
GSE54825 Transcriptional reprogramming of engineered cellobiose-utilizing Saccharomyces cerevisiae in response to cellobiose revealed by RNA-Seq
Affiliated with GSE69404
BioSample SAMN02639514
SRA SRX468698

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap