|
| Status |
Public on Jun 29, 2010 |
| Title |
segment 3 rep 4 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Zebrafish intestine tissue
|
| Organism |
Danio rerio |
| Characteristics |
sample type: segment 3 rep 4
tissue: intestine
|
| Growth protocol |
Zebrafish were reared at room temperature (27°C)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of tissue samples were extracted using Trizol reagent (Invitrogen) according to the manufacturers instructions.
|
| Label |
Cy5
|
| Label protocol |
For fluorescence labeling of cDNAs, 20 µg of total RNA from the reference and experimental samples were reverse transcribed in the presence of Cy3-dUTP and Cy5-dUTP (Amersham Inc.), respectively. Labeled cDNA were pooled, concentrated, and resuspended in DIG EasyHyb (Roche Applied Science) buffer for hybridization.
|
| |
|
| Channel 2 |
| Source name |
whole zebrafish tissue
|
| Organism |
Danio rerio |
| Characteristics |
sample type: Reference RNA was obtained by pooling male and female total RNA from wild-type zebrafish at a ratio of 9:1.
|
| Growth protocol |
Zebrafish were reared at room temperature (27°C)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of tissue samples were extracted using Trizol reagent (Invitrogen) according to the manufacturers instructions.
|
| Label |
Cy3
|
| Label protocol |
For fluorescence labeling of cDNAs, 20 µg of total RNA from the reference and experimental samples were reverse transcribed in the presence of Cy3-dUTP and Cy5-dUTP (Amersham Inc.), respectively. Labeled cDNA were pooled, concentrated, and resuspended in DIG EasyHyb (Roche Applied Science) buffer for hybridization.
|
| |
|
| |
| Hybridization protocol |
Reference RNA was obtained by pooling equal amount of total RNA extracted from male and female wildtype fish. Reference RNA is co-hybridized with RNA samples extracted either from treated or control fish on a glass array spotted with 16,416 zebrafish oligo probes (16,244 LEADS clusters and 172 copies of β-actin controls)
|
| Scan protocol |
The arrays were scanned using the GenePix 4000B microarray scanner (Axon Instruments, USA) and the generated images with their fluorescence signal intensities were analyzed using GenePix Pro 4.0 image analysis software (Axon Instruments, USA).
|
| Description |
Biological replicate 4 of 5: segment 3
|
| Data processing |
The data were global median normalized, then log2 ratio of means obtained as defined by CH1/CH2.
|
| |
|
| Submission date |
Mar 15, 2010 |
| Last update date |
Jun 29, 2010 |
| Contact name |
zhengyuan wang |
| E-mail(s) |
[email protected]
|
| Phone |
+65-6516-8940
|
| Organization name |
National University of Singapore
|
| Department |
Biological Sciences
|
| Lab |
Gong Zhiyuan's Lab
|
| Street address |
14 Science Drive 4
|
| City |
Singapore |
| ZIP/Postal code |
117543 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL10182 |
| Series (1) |
| GSE20884 |
Morphological and molecular evidence that the zebrafish intestine is organized into a small and large intestine |
|
