|
| Status |
Public on Dec 22, 2014 |
| Title |
32°C treatment (T2) vs. 28°C control (T1) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
T2
|
| Organism |
Stylophora pistillata |
| Characteristics |
temperature: 32°C
|
| Treatment protocol |
The experimental aquarium was subjected to an increase of 1°C per day, from 24°C to 34°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol ,the samples were further purified using an RNA Clean and Concentrator kit (Zymo Research).
|
| Label |
Cy3
|
| Label protocol |
200 ng of total RNA, in the presence of control RNAs (RNA spike-in kit; Agilent), for each sample was labeled with either Cy-3 or Cy-5 using the Low Input Quick Amp Labeling Kit, two-color (Agilent) following the manufacturer’s protocol.
|
| |
|
| Channel 2 |
| Source name |
T1
|
| Organism |
Stylophora pistillata |
| Characteristics |
temperature: 28°C
|
| Treatment protocol |
The experimental aquarium was subjected to an increase of 1°C per day, from 24°C to 34°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol ,the samples were further purified using an RNA Clean and Concentrator kit (Zymo Research).
|
| Label |
Cy5
|
| Label protocol |
200 ng of total RNA, in the presence of control RNAs (RNA spike-in kit; Agilent), for each sample was labeled with either Cy-3 or Cy-5 using the Low Input Quick Amp Labeling Kit, two-color (Agilent) following the manufacturer’s protocol.
|
| |
|
| |
| Hybridization protocol |
Equal amounts of labeled RNA were then hybridized on the chip, per the Agilent protocol, at 60 degrees overnight. The hybridization mixes were prepared using the Gene Expression Hybridization Kit from Agilent following the manufacturer’s protocol. After hybridization, the slide was washed first with Gene Expression Wash Buffer 1(Agilent) and then Gene Expression Wash Buffer 2(Agilent). This was followed by a acetonitrile wash and finally the slides were placed in Stabilization& Drying Solution (Agilent). The washed slides were scanned on on an Agilent G2565BA scanner. Feature extraction was performed using the Feature extraction software from Agilent
|
| Scan protocol |
Scanned on an Agilent G2565BA microarray scanner
|
| Description |
32°C treatment (T2) vs. 28°C control (T1). Technical replicates
|
| Data processing |
The data from all arrays were first subjected to background correction and LOESS within-array normalization using Agilent Feature Extraction software (version 9.5.1.1 Agilent Technologies, Santa Clara, CA). The rest of the analysis was performed in Partek® Genomics Suite software, version 6.6 Copyright © 2012 Partek Inc., St. Louis, MO, USA.The log expression ratios that were produced during the normalization step were analyzed.
|
| |
|
| Submission date |
Jun 10, 2013 |
| Last update date |
Dec 22, 2014 |
| Contact name |
Hiba Waldman Ben-Asher |
| Organization name |
Bar-Ilan University
|
| Department |
Life-Sciences
|
| Street address |
Ramat-Gan
|
| City |
Ramat-Gan |
| ZIP/Postal code |
52900 |
| Country |
Israel |
| |
|
| Platform ID |
GPL17270 |
| Series (1) |
| GSE47779 |
Gene expression profile of ‘heat stress’ in the Red Sea coral Stylophora pistillata |
|
