|
| Status |
Public on Feb 19, 2009 |
| Title |
T6 vs T2 first biological replica |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
T21
|
| Organism |
Mytilus galloprovincialis |
| Characteristics |
treatment: Okadaic acid
age: 1 week post treatment
biological replica: 1
tissue: digestive gland
|
| Treatment protocol |
6.5 µg of Okadaic acid (Sigma Chemical Co.) diluted in 1 mL ethanol every two days for a time span of 5 weeks
|
| Growth protocol |
Mussels were maintained in tanks provided with oxygen-pump and water-lively pump in sea water. To prevent additional environmental stress, the seasonal photoperiod (L 10-D 14) and water temperature (17°C) were maintained. Sea water was changed weekly and water salinity (37 PSU) was controlled daily.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using RNAtidy G following manufacturer's instructions plus an additional LiCl precipitation
|
| Label |
Cy3
|
| Label protocol |
Total RNA was retro-transcribed using Superscript II Reverse Transcriptase (Invitrogen) with aminoallyl-dUTP and then labelled with Cy5 or Cy3 fluorescent dyes (GE Healthcare)
|
| |
|
| Channel 2 |
| Source name |
T61
|
| Organism |
Mytilus galloprovincialis |
| Characteristics |
treatment: Okadaic acod
age: 5 weeks post treatment
biological replica: 1
tissue: digestive gland
|
| Treatment protocol |
6.5 µg of Okadaic acid (Sigma Chemical Co.) diluted in 1 mL ethanol every two days for a time span of 5 weeks
|
| Growth protocol |
Mussels were maintained in tanks provided with oxygen-pump and water-lively pump in sea water. To prevent additional environmental stress, the seasonal photoperiod (L 10-D 14) and water temperature (17°C) were maintained. Sea water was changed weekly and water salinity (37 PSU) was controlled daily.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using RNAtidy G following manufacturer's instructions plus an additional LiCl precipitation
|
| Label |
Cy5
|
| Label protocol |
Total RNA was retro-transcribed using Superscript II Reverse Transcriptase (Invitrogen) with aminoallyl-dUTP and then labelled with Cy5 or Cy3 fluorescent dyes (GE Healthcare)
|
| |
|
| |
| Hybridization protocol |
labelled cDNAs were hybridised in SSC 5X, Sarcosile 0.1%, Denhardt sol 1X overnight at 48°C, the slides were washed with decreasing stringency buffer untill SSC 0.05X.
|
| Scan protocol |
Bio-Rad Chip Reader, laser powers 100% and detector sensitivity varied to balance the two channel intensities
spots were inspected and quantified with Bio-Rad Cheap Reader's software.
|
| Description |
Digestive gland responses to okadaic acid treatment, loop design
|
| Data processing |
Raw data was first background subtracted then normalized with the LOESS algorithm. Finally a quantile normalization was apply. R software was used implemented with LIMMA package
|
| |
|
| Submission date |
Feb 18, 2009 |
| Last update date |
Feb 18, 2009 |
| Contact name |
Rene Dreos |
| E-mail(s) |
rene.dreos@unil.ch
|
| Phone |
0044 (0)1603 450793
|
| Organization name |
UNIL
|
| Department |
CIG
|
| Lab |
Gatfield Lab
|
| Street address |
Ecublens
|
| City |
Lausanne |
| State/province |
VD |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL1799 |
| Series (1) |
| GSE14885 |
Time course study of Mediterranean mussel (M. galloprovincialis, Lmk, 1819) digestive gland treated with okadaic acid |
|
