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Sample GSM1324497

Query DataSets for GSM1324497

Status

Public on Apr 10, 2015

Title

JCYL002B

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 (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.

Submission date

Feb 10, 2014

Last update date

May 15, 2019

Contact name

Yuping Lin

E-mail(s)

lin_yp@tib.cas.cn

Organization name

Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

Street address

32 West 7th Avenue, Tianjin Airport Economic Area