|
| Status |
Public on Mar 31, 2014 |
| Title |
R008_45gl |
| Sample type |
SRA |
| |
|
| Source name |
Yeast culture
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: R008
carbon dioxide produced before cell collection [g/l]: 45
|
| Growth protocol |
Yeast cultures were grown in 100 ml YPD medium at 25 °C in agitation for 18 hours. Each culture have been centrifuged and the pellet was resuspended into the volume of synthetic must MS300 required to obtain an OD600 of 0.5 of the 1:10 diluted solution (5x10^6 cells/ml). 100 ml of this pre-inoculum have been added to 900 ml of MS300, a synthetic medium that mimics the composition of a white wine must. Fermentation was performed at 25°C in 1 l bioreactors (Multifors, Infors HT) monitoring the temperature, the pH, and the CO2 flux in a range of 1-20 ml/min (red-y mod. GSM-A95A-BN00). Yeast cells were collected at two different steps of the fermentation curve: at the beginning of the process, when the CO2 produced by the cells was 6 g/l (middle exponential growth phase), and in the middle of fermentation, at 45 g/l (early stationary phase).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For total RNA extraction we used the "PureLink RNA Mini Kit" (life technologies). Starting from 10 μgs of total RNA, 18S and 26S rRNAs were removed using the RiboMinusTM Transcriptome Isolation Kit (Invitrogen). RNA molecules were decapped with the TAP enzyme (Wako Chemicals) resuspending the samples of purified total RNA into 12 μl of water and adding the 5X TAP buffer plus 10 U of TAP enzyme and incubating the reaction at 37°C for 40 minutes. Genomic DNA was removed using the DNA-free™ kit from Applied Biosystems. The RNA was used to prepare the libraries using the SOLiD 4 Whole Transcriptome Analysis Kit protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD 4 System |
| |
|
| Description |
vineyard strain (wild type) R008
|
| Data processing |
SOLiD reads were aligned using PASS software; only those uniquely aligned on the genome were considered
The number of reads aliged on each gene for each strain and sample was determined using a self-written perl script and an input file for DEGseq was generated
Differentially expressed genes were determined using DEGseq software 2.11.1
Genome_build: Saccharomyces cerevisiae sacCer2.61
Supplementary_files_format_and_content: tab-delimited text file includes the RKPM value for each strain and sample normalized considering S288c sample at middle exponential phase (6 g/l of CO2 produced) as a reference and considering the total number of reads aligned for each experiment
|
| |
|
| Submission date |
Mar 04, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Stefano Campanaro |
| E-mail(s) |
stefano.campanaro@gmail.com
|
| Phone |
+39 049 827 6306
|
| Organization name |
University of Padua
|
| Department |
Biology
|
| Street address |
Via Ugo Bassi 58/b
|
| City |
Padova |
| ZIP/Postal code |
35121 |
| Country |
Italy |
| |
|
| Platform ID |
GPL15263 |
| Series (1) |
| GSE44845 |
Comparison of vineyard, enological and laboratory yeast transcriptomes at different steps of the fermentation curve |
|
| Relations |
| SRA |
SRX248455 |
| BioSample |
SAMN01974753 |
