|
| Status |
Public on Oct 06, 2014 |
| Title |
Untreated-repetition1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Klyap8∆-Untreated
|
| Organism |
Kluyveromyces lactis |
| Characteristics |
strain: Klyap8∆
treatment: Untreated
|
| Treatment protocol |
Cells were exposed or not to a stress for 30 min: 0.1 mM sodium arsenite, NaASO2 or 0.25 mM t-BOOH
|
| Growth protocol |
K. lactis cells exponentially grown in YPD medium were exposed or not to a stress for 30 min. The cells were harvested, pelleted and frozen for further analysis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by trizol treatment following manufacturer's instructions (Invitrogen, Carlsbad, CA, USA)
|
| Label |
Cy3
|
| Label protocol |
RNA was linearly amplified and labeled with two different fluorescent dyes ; cyanine 3-CTP (cy-3) and cyanine5-CTP (cy-5), using the Agilent Low Input Quick Amp Labelling kit (version 6.5, May 2010)
|
| |
|
| Channel 2 |
| Source name |
Klwt-Untreated (reference)
|
| Organism |
Kluyveromyces lactis |
| Characteristics |
strain: Klwt
treatment: Untreated
|
| Treatment protocol |
Cells were exposed or not to a stress for 30 min: 0.1 mM sodium arsenite, NaASO2 or 0.25 mM t-BOOH
|
| Growth protocol |
K. lactis cells exponentially grown in YPD medium were exposed or not to a stress for 30 min. The cells were harvested, pelleted and frozen for further analysis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by trizol treatment following manufacturer's instructions (Invitrogen, Carlsbad, CA, USA)
|
| Label |
cy5
|
| Label protocol |
RNA was linearly amplified and labeled with two different fluorescent dyes ; cyanine 3-CTP (cy-3) and cyanine5-CTP (cy-5), using the Agilent Low Input Quick Amp Labelling kit (version 6.5, May 2010)
|
| |
|
| |
| Hybridization protocol |
Hybridizations were performed as recommended by the manufacturer (Two-Colour Microarray-Based Gene Protocol, version 6.5, May 2010, from Agilent Technologies). 300 ng of Cy-3 and Cy-5 labelled cRNA were combined with 10x blocking agent, and 25x fragmentation buffer at 60ºC for exactly 30 min. The reaction was stopped with 2x GE hybridization buffer HI-RPM and hybridized to the oligo microarray for 17 h at 65ºC with continuing rotation (10 r.p.m). After hybridization, slides were washed for 1 min at room temperature, using GE wash buffer 1, and 1 min at 37ºC with GE wash buffer 2.
|
| Scan protocol |
Agilent G2565 Scanner in extended dynamic range with a resolution of 5 nm per pixel
The scanned images were quantified using Agilent Feature Extraction Software (version10.7.3.1).
|
| 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. Differental analysis was performed with the varmixt package of R.
|
| |
|
| Submission date |
Feb 18, 2014 |
| Last update date |
Oct 07, 2014 |
| Contact name |
Djamila Onesime |
| E-mail(s) |
donesime@grignon.inra.fr
|
| Organization name |
INRA
|
| Department |
MICA
|
| Lab |
Micalis, 1319
|
| Street address |
CBAI
|
| City |
Thiverval - Grignon |
| ZIP/Postal code |
78850 |
| Country |
France |
| |
|
| Platform ID |
GPL11307 |
| Series (1) |
| GSE55128 |
Exploring the response of Kluyveromyces lactis to arsenite and peroxide stress and the role of the transcription factor KlYap8 and KlYap1 |
|
