|
| Status |
Public on Mar 30, 2015 |
| Title |
R2 IVo vs Sc1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
R2 IVo
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: Intraspecific hybrid
|
| Treatment protocol |
Industrial cultivation and drying were performed according to the Laboratory of Research and Development (Lallemand S.A.S.) standard protocols.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA, extracted as described in Querol et al. [15], was resuspended in 50μl of de-ionized water and digested with endonuclease Hinf I (Roche Applied Science, Germany), according to the manufacturer’s instructions, to fragments of an average length of 0.25 to 8 kbp. Each sample was purified using High pure PCR Product Purification Kit (Roche Applied Science, Germany)
|
| Label |
Cy3,Cy5
|
| Label protocol |
2μg was labelled using BioPrime Array CGH Genomic Labelling System (Invitrogen, California,USA). Unincorporated label was removed using MinElute PCR Purification Kit (Qiagen, Germany). Equal amounts of labelled DNA from the strains to be compared were used as probes for microarray hybridization.
|
| |
|
| Channel 2 |
| Source name |
Sc1
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: Parental strain 1
|
| Treatment protocol |
Industrial cultivation and drying were performed according to the Laboratory of Research and Development (Lallemand S.A.S.) standard protocols.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA, extracted as described in Querol et al. [15], was resuspended in 50μl of de-ionized water and digested with endonuclease Hinf I (Roche Applied Science, Germany), according to the manufacturer’s instructions, to fragments of an average length of 0.25 to 8 kbp. Each sample was purified using High pure PCR Product Purification Kit (Roche Applied Science, Germany)
|
| Label |
Cy5,Cy3
|
| Label protocol |
2μg was labelled using BioPrime Array CGH Genomic Labelling System (Invitrogen, California,USA). Unincorporated label was removed using MinElute PCR Purification Kit (Qiagen, Germany). Equal amounts of labelled DNA from the strains to be compared were used as probes for microarray hybridization.
|
| |
|
| |
| Hybridization protocol |
Array competitive genomic hybridization (aCGH) was performed using a double-spotted array containing 6,240 ORFs of Saccharomyces cerevisiae plus control spots totaling 6.4 K (Microarray Centre, University Health Network, Toronto, Canada). New microarrays were pre-treated for one hour at 65°C with pre-hybridization solution (7.5 ml 20× SSC, 0.5 ml 10% SDS, 0.5 ml 10 mg/ml bovine serum albumin in 50 ml final volume). Pre-hybridization solution was washed during 15 s in mili-Q H2O, 2 s in 2-propanol, 2 s in milli-Q H2O and dried by centrifugation at 1200 rpm, 10 min. Microarrays were treated with hybridization solution (15μl SSC, 0.6μl 10% SDS, 6μl 1 mg/ml salmon DNA and DNA labelled in 60μl final volume) at 95°C for 1 min and at room temperature for 5 min before DNA hybridization. Hybridization was performed for 18 h in chamber at 65°C.
|
| Scan protocol |
Microarray scanning was carried out using a GenePix Personal 4100A scanner (Axon Instruments/Molecular Devices Corp., USA).
|
| Description |
Duplicate arrays and Cy5-dCTP and Cy3-dCTP dye-swap assays
|
| Data processing |
Microarray images and raw data were produced using the GenePix Pro 6.1 software (Axon Instruments/Molecular Devices Corp.) and the background was subtracted by applying the local feature background median option. M-A plots (M = Log2 ratios; A = log2 of the product of intensities) were represented in order to evaluate if the ratio data were intensity-dependent.
|
| |
|
| Submission date |
Jun 19, 2013 |
| Last update date |
Mar 30, 2015 |
| Contact name |
Laura Pérez Través |
| E-mail(s) |
laupetra@iata.csic.es
|
| Organization name |
IATA
|
| Street address |
Avda Catedrático Agustín Escardino
|
| City |
Paterna (Valencia) |
| ZIP/Postal code |
46980 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13945 |
| Series (1) |
| GSE48117 |
Physiological and genomic analysis of Saccharomyces cerevisiae artificial hybrids with improved fermentation performance and mannoprotein release capacity |
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