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Status |
Public on Jan 11, 2022 |
Title |
Evolved cells, repl2 |
Sample type |
RNA |
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|
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
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|
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Hybridization protocol |
Labeled cDNAs were processed with GeneChip® IVT PLUS Reagent Kit (Affymetrix®) and hybridized with GeneChip™ Yeast Genome 2.0 Array
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Scan protocol |
GeneChips were scanned using the GeneChip® Scanner 3000 7G (Affymetrix®)
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Description |
Gene expression data from evolved cells collected after 4 h of fermentation in presence of insoluble solids and lignocellulose-derived inhibitors
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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
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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 |
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