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Sample GSM1025315 Query DataSets for GSM1025315
Status Public on Feb 02, 2015
Title PE2_flocculate_3hrs
Sample type SRA
 
Source name FL1
Organism Saccharomyces cerevisiae
Characteristics fermentation time: 3 hours of fermentation
strain: PE-2
fermentation condition: flocculate industrial fermentation
Growth protocol Yeasts were collected directly from industrial fermentation tanks of sugarcane ethanol production
Extracted molecule total RNA
Extraction protocol Pools of biological material were obtained mixing the three biological replicates for each time-point. Total RNA of 13 fermentation time-points was extracted using phenol and chloroform.
RNA-seq libraries were prepared from 1 µg total RNA following the manufacturer`s protocol (Illumina). Briefly, mRNA was isolated using oligo(dt) magnetic beads and fragmented in the presence of divalent zinc ions. Fragmented RNA was then used for first and second strands cDNA synthesis. Double-stranded cDNA was end-repaired and 3` adenylated for ligation of sequence adapters. After ligation of adapters, fragments of approximately 250 bp were isolated by gel electrophoresis and PCR amplified.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
 
Description SRX174770
Data processing Libraries were validated on an Experion DNA chip (Bio-Rad) and quantified using a Qubit fluorometer (Invitrogen).
Each RNA-seq library was sequenced in one lane of an Illumina Genome Analyzer II sequencer, which produced ~20-30 million reads (36 bp single-end).
For each RNA-seq library, reads were aligned against a reference gene database constituted by S. cerevisiae S288C genes (www.yeastgenome.org).
The alignment was performed by SOAPaligner version 2.20 allowing up to 2 base mismatches and discarding repeat reads.
After that, a Perl script was made to calculate the number of reads aligned by genes for each RNA-seq library. The output file was analyzed by DEGSeq package (R Bioconductor) for identification of differentially expressed (DE) genes between libraries.
Gene expression levels were determined using RPKM formula.
Gene ontology (GO) terms of DE genes were obtained by SGD database (http://www.yeastgenome.org/cgi-bin/GO/goSlimMapper.pl) using Yeast GO-Slim Process parameters and cutoff p-value < 0.01.
Genome_build: S. cerevisiae S288c
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
 
Submission date Oct 25, 2012
Last update date May 15, 2019
Contact name Osmar Netto
E-mail(s) osmar@granbio.com.br
Organization name Genomic and Expression Laboratory
Street address UNICAMP
City campinas
ZIP/Postal code 13083-970
Country Brazil
 
Platform ID GPL9377
Series (1)
GSE41834 Genome-wide transcriptional analysis of PE-2 strain of Saccharomyces cerevisiae
Relations
BioSample SAMN02197206
SRA SRX174770

Supplementary file Size Download File type/resource
GSM1025315_rpkm_FL1.txt.gz 51.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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