|
| Status |
Public on Feb 02, 2015 |
| Title |
PE2_typical_12hrs |
| Sample type |
SRA |
| |
|
| Source name |
TF5
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
fermentation time: 12 hours of fermentation
strain: PE-2
fermentation condition: typical 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 |
SRX174773
|
| 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 |
SAMN02197261 |
| SRA |
SRX174773 |
