|
| Status |
Public on Oct 01, 2011 |
| Title |
Cystine-repetition3-dye swap |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
growth on 1mM cystine
|
| Organism |
Kluyveromyces lactis |
| Characteristics |
growth medium: 1mM cystine
|
| Growth protocol |
K. lactis cells were grown in exponential growth for ten generations thanks to transfer on fresh medium. The growth medium is a chemically defined medium according to Mansour et al. Appl. Env. Microbiol. (2008) 74:6505-6512.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by trizol treatment following manufacturer's instructions (Invitrogen, Carlsbad, CA, USA)
|
| Label |
Alexa555
|
| Label protocol |
RNA was labeled using the Superscript indirect cDNA labeling system kit (Invitrogen) with anchored oligo(dT)20 primer according to manufacturer's instructions
|
| |
|
| Channel 2 |
| Source name |
growth on 1µM cystine
|
| Organism |
Kluyveromyces lactis |
| Characteristics |
growth medium: 1µM cystine
|
| Growth protocol |
K. lactis cells were grown in exponential growth for ten generations thanks to transfer on fresh medium. The growth medium is a chemically defined medium according to Mansour et al. Appl. Env. Microbiol. (2008) 74:6505-6512.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by trizol treatment following manufacturer's instructions (Invitrogen, Carlsbad, CA, USA)
|
| Label |
Alexa647
|
| Label protocol |
RNA was labeled using the Superscript indirect cDNA labeling system kit (Invitrogen) with anchored oligo(dT)20 primer according to manufacturer's instructions
|
| |
|
| |
| Hybridization protocol |
hybridizations were performed for 17h at 65°C in dedicated micro-chambers with 80pmol of the different labelled samples.hybridization buffer was from Agilent (ref 5188-5242)
|
| Scan protocol |
Agilent G2565 Scanner in extended dynamic range with a resolution of 5nm per pixel
|
| Description |
originally submitted ratio value represents µM/mM
|
| Data processing |
intensity-dependent normalization was performed with the LOESS procedure followed by subtraction of the log-ratio median calculated over the values for an entire block from each individual log-ratio using the anapuce package of R. Differential analysis was performed with the varmixt package of R.
the raw P values were adjustred by the Benjamini-Hochberg method
genes with both a P-value < 0,05 and a ratio higher than 2 were considered as diffrentially expressed
|
| |
|
| Submission date |
Dec 10, 2010 |
| Last update date |
Oct 01, 2011 |
| Contact name |
Jean-Marie Beckerich |
| E-mail(s) |
Jean-Marie.Beckerich@grignon.inra.fr
|
| Phone |
00 33 01 30 81 54 43
|
| Organization name |
INRA
|
| Lab |
MICALIS
|
| Street address |
Campus Agroparistech
|
| City |
Thiverval-Grignon |
| ZIP/Postal code |
78850 |
| Country |
France |
| |
|
| Platform ID |
GPL11307 |
| Series (1) |
| GSE26013 |
Exploration of the sulfur metabolism in the yeast Kluyveromyces lactis |
|
