|
| Status |
Public on Dec 03, 2007 |
| Title |
K3_Slide2B_9Cy3_3Cy5 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Porcine epithelial cells (PK15)
|
| Organism |
Sus scrofa |
| Characteristics |
Time (h) post-infection: 2
Replicate: 1
Status: Mock-Infected
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were extracted using Trizol (Invitrogen)-chlorofrom method.
|
| Label |
Cy3
|
| Label protocol |
Five µg of each RNA were reverse-transcribed and labelled with Cy3 and Cy5 (reagents: Pronto kit, Corning and Amersham, Biosciences). Labelled targets were quantified (Nanodrop, Nyxor Biotech), evaporated and the pellets were resuspended in hybridization buffer (Pronto Kit, Corning) at a final concentration of 2 pmoles/µl. Control RNA (Spikes, Lucidea Universal Scorecard, Amersham Biosciences) specific of control spots on the SLA slides were labelled together with total RNA.
|
| |
|
| Channel 2 |
| Source name |
Porcine epithelial cells (PK15)
|
| Organism |
Sus scrofa |
| Characteristics |
Time (h) post-infection: 2
Replicate: 1
Status: PrV-Infected
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were extracted using Trizol (Invitrogen)-chlorofrom method.
|
| Label |
Cy5
|
| Label protocol |
Five µg of each RNA were reverse-transcribed and labelled with Cy3 and Cy5 (reagents: Pronto kit, Corning and Amersham, Biosciences). Labelled targets were quantified (Nanodrop, Nyxor Biotech), evaporated and the pellets were resuspended in hybridization buffer (Pronto Kit, Corning) at a final concentration of 2 pmoles/µl. Control RNA (Spikes, Lucidea Universal Scorecard, Amersham Biosciences) specific of control spots on the SLA slides were labelled together with total RNA.
|
| |
|
| |
| Hybridization protocol |
The slides were pre-soaked, prehybridized and hybridized with the same quantity of Cy3 and Cy5 labelled cDNAs : 20 pmoles of each labelled cDNAs (Pronto Kit, Corning). After 16 hours hybridization at 42-b°C, the slides were washed according to commercial protocol (Pronto kit, Corning) and dried by centrifugation (1500 rpm, 3 min).
|
| Scan protocol |
Slides were scanned on the Scanarray scanner (Perkin Elmer). Signals were quantified with the Imagene 5.1 software (Biodiscovery).
|
| Description |
slide 13309378
|
| Data processing |
The normalisation steps was performed using scripts written with R software. Raw data were log2 transformed, normalized by lowess (f=0.3) and the median of each block spotted on slide was substracted.
|
| |
|
| Submission date |
Aug 03, 2007 |
| Last update date |
Sep 24, 2007 |
| Contact name |
Laurence Flori |
| E-mail(s) |
laurence.flori@jouy.inra.fr
|
| Organization name |
INRA
|
| Department |
Génétique Animale
|
| Lab |
LREG
|
| Street address |
Domaine de Vilvert
|
| City |
Jouy en Josas |
| ZIP/Postal code |
78350 |
| Country |
France |
| |
|
| Platform ID |
GPL5622 |
| Series (1) |
| GSE8676 |
PrV/PK15 kinetics_SLA/PrV slides |
|
| Data table header descriptions |
| ID_REF |
|
| VALUE |
Normalized signal measurement for each hybridized spot |
| CH1_MEDIAN |
channel 1 signal intensity median - Cy3 |
| CH1_MEAN |
channel 1 signal intensity mean |
| CH1_SD |
channel 1 signal intensity standard deviation |
| CH1_BKD_MEDIAN |
channel 1 background signal intensity median |
| CH1_BKD_MEAN |
channel 1 background signal intensity mean |
| CH1_BKD_SD |
channel 1 background signal intensity standard deviation |
| CH2_MEDIAN |
channel 2 signal intensity median - Cy5 |
| CH2_MEAN |
channel 2 signal intensity mean |
| CH2_SD |
channel 2 signal intensity standard deviation |
| CH2_BKD_MEDIAN |
channel 2 background signal intensity median |
| CH2_BKD_MEAN |
channel 2 background signal intensity mean |
| CH2_BKD_SD |
channel 2 background signal intensity standard deviation |
| FLAGS |
|
