|
| Status |
Public on Dec 09, 2015 |
| Title |
Mg1-REF-1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
yeast cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: JP1
treatment: 500 mg/L of magnesium (Mg2+ medium)
|
| Treatment protocol |
Fermentation assays was performed with the industrial yeast S. cerevisiae JP1 in reference medium (mineral concentration balanced), in the medium supplemented with 500 mg/L of magnesium (Mg2+ medium) and in the medium supplemented with 1 mg/L of copper (Cu2+ medium).
|
| Growth protocol |
The cell was growth in YPD medium at 30ºC and 150 rpm in a rotatory shaker until a cell concentration of 25g/L to start the fermentation assay.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA extraction was carried out with the rupture of the yeast cells with AE buffer and SDS10% in 65ºC and purified with the Maxwell 16LEV simplyRNA blood Kit.
|
| Label |
Cy5
|
| Label protocol |
Synthesis of cDNA and labelling was performed by Two-Color Low Input Quick Amp Labeling Kit (cat. nr. 5190-2306, Agilent, USA), with Two-Color RNA spike-in kit for internal control (cat. nr. 5188-5279, Agilent, USA). For yeast samples, 100 ng of purified RNA was used for labelling.
|
| |
|
| Channel 2 |
| Source name |
yeast cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: JP1
sample type: reference
treatment: none
|
| Treatment protocol |
Fermentation assays was performed with the industrial yeast S. cerevisiae JP1 in reference medium (mineral concentration balanced), in the medium supplemented with 500 mg/L of magnesium (Mg2+ medium) and in the medium supplemented with 1 mg/L of copper (Cu2+ medium).
|
| Growth protocol |
The cell was growth in YPD medium at 30ºC and 150 rpm in a rotatory shaker until a cell concentration of 25g/L to start the fermentation assay.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA extraction was carried out with the rupture of the yeast cells with AE buffer and SDS10% in 65ºC and purified with the Maxwell 16LEV simplyRNA blood Kit.
|
| Label |
Cy3
|
| Label protocol |
Synthesis of cDNA and labelling was performed by Two-Color Low Input Quick Amp Labeling Kit (cat. nr. 5190-2306, Agilent, USA), with Two-Color RNA spike-in kit for internal control (cat. nr. 5188-5279, Agilent, USA). For yeast samples, 100 ng of purified RNA was used for labelling.
|
| |
|
| |
| Hybridization protocol |
RNA from the cells fermented with reference medium were labelled with Cy3 and mixed with Cyb5-labelled RNA from the cells fermented with Mg2+ medium and Cu2+ medium. Target and reference cRNA samples were mixed and the hybridizations were performed on yeast gene expression 8x15K spots slides (cat. nr. G4813A-016322, Agilent, USA) at 65 ºC for 17 hours at 10 r.pm. in the Microarray Hybridization Oven (cat. nr. G2545A, Agilent, USA).
|
| Scan protocol |
The slides were placed into the High-Resolution Microarray Scanner (cat. nr. G2505-60502, Agilent, USA). The fluorescence data were extracted (.txt files) for each spot by using Scan Control 8.5.1 software (Agilent, USA)
|
| Data processing |
Data were then analyzed using specific packages from the R statistical language with the specific LIMMA and MArray packages. Background correction was done with normexp method. Robust spline and quantile methods were used for normalization within and between arrays, respectively. A list of differentially expressed genes was generated by applying adjusted p-values for multiple tests. Groups of genes with statistical significance (Adj.p<0.05) were utilized.
|
| |
|
| Submission date |
Dec 08, 2015 |
| Last update date |
Dec 09, 2015 |
| Contact name |
Marcos Antonio Morais |
| E-mail(s) |
marcos.morais@pesquisador.cnpq.br
|
| Organization name |
Federal University of Pernambuco
|
| Department |
Department of Genetics
|
| Lab |
Interdepartmental Research Group in Metabolic Engineering
|
| Street address |
Av. Moraes Rego, 1235
|
| City |
Recife |
| State/province |
Pernambuco |
| ZIP/Postal code |
50670-901 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL16244 |
| Series (1) |
| GSE75803 |
The effect of the magnesium and copper supplementation in the transcriptional response of Saccharomyces cerevisiae JP1 under fermentation condition |
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