|
| Status |
Public on Jun 29, 2017 |
| Title |
C11 biological rep2 vs. T11 biological rep2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
C11
|
| Organism |
Stylophora pistillata |
| Characteristics |
treated with: natural concentration of calcium (SW)
time point: mid-day (11:00)
tissue: coral fragments
|
| Treatment protocol |
Coral fragments of Stylophora pistillata were incubated for 1.5 hours in two different calcium concentrations natural calcium concentration (SW) and natural calcium concentration add with 100 mg/L (SW+100). Three coral fragments, for each treatment and time point, were sampled after the incubation, snap froze in liquid nitrogen and stored in -80 C until further handled.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol
|
| 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 |
T11
|
| Organism |
Stylophora pistillata |
| Characteristics |
treated with: additional 100mg/L calcium (SW+100)
time point: mid-day (11:00)
tissue: coral fragments
|
| Treatment protocol |
Coral fragments of Stylophora pistillata were incubated for 1.5 hours in two different calcium concentrations natural calcium concentration (SW) and natural calcium concentration add with 100 mg/L (SW+100). Three coral fragments, for each treatment and time point, were sampled after the incubation, snap froze in liquid nitrogen and stored in -80 C until further handled.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol
|
| 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 |
C11_T11_1_2
|
| 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 |
Sep 21, 2016 |
| Last update date |
Jun 29, 2017 |
| 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) |
| GSE87159 |
Identifying Genes Associated with the Molecular Scleractinian Coral Calcification Process (Stylophora pistillata study case) |
|
