|
| Status |
Public on Jan 11, 2022 |
| Title |
Evolved cells, repl3 |
| Sample type |
RNA |
| |
|
| Source name |
Evolved cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain background: F12
strain: evolved
|
| Growth protocol |
Fermentation was performed in YNB medium (Conda, Cat.1553.00) supplemented with 20 g/L glucose and 7.5 g/L (NH4)2SO4 in presence of 40% (w/w) insoluble solids and a inhibitory mix (2.1 g/L furfural, 0.3 g/L 5-HMF, 13.4 g/L acetic acid, 10.5 g/L formic acid, 0.4 g/L ferulic acid, 0.2 g/L syringaldehyde, and 0.1 g/L vanillin).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cDNAs were prepared according to the standard Affymetrix protocol
|
| |
|
| Hybridization protocol |
Labeled cDNAs were processed with GeneChip® IVT PLUS Reagent Kit (Affymetrix®) and hybridized with GeneChip™ Yeast Genome 2.0 Array
|
| Scan protocol |
GeneChips were scanned using the GeneChip® Scanner 3000 7G (Affymetrix®)
|
| Description |
Gene expression data from evolved cells collected after 4 h of fermentation in presence of insoluble solids and lignocellulose-derived inhibitors
|
| Data processing |
Raw data were processed with RMA algorithm included in Affymetrix® Expression Console™ for normalization and gene level analysis. Fold changes between experimental conditions were calculated as a quotient between the mean of the gene expression signals. Statistical analysis was performed with LIMMA package included in Babelomics software package
logFC_data.txt: Raw data were processed with Bioconductor online Piano software, using FDR for multiple testing adjustment and a P-value cuttoff of 0.05; Summary topTable() with False Discovery Rate adjustment
|
| |
|
| Submission date |
Oct 07, 2020 |
| Last update date |
Jan 11, 2022 |
| Contact name |
Antonio David Moreno |
| E-mail(s) |
david.moreno@ciemat.es
|
| Phone |
+34 91 346 6054
|
| Organization name |
CIEMAT
|
| Department |
Department of Energy
|
| Lab |
Biofuels Unit
|
| Street address |
Avda. Complutense 40
|
| City |
Madrid |
| ZIP/Postal code |
28040 |
| Country |
Spain |
| |
|
| Platform ID |
GPL2529 |
| Series (1) |
| GSE159167 |
Expression data from parental and evolved Saccharomyces cerevisiae F12 cells in the presence of insoluble solids at high concentration and lignocellulose-derived inhibitors |
|
