|
| Status |
Public on Feb 13, 2017 |
| Title |
28_L05_J |
| Sample type |
RNA |
| |
|
| Source name |
trunk, juvenile, control temperature
|
| Organism |
Danio rerio |
| Characteristics |
tissue: trunk
temperature (oc): 28
age (dpf): 37
|
| Treatment protocol |
Zebrafish were exposed to either high (36 oC) or control (28 oC) temperature from 18 to 32 dpf. After treatment the fish were reared at 28 oC until sampling at 37 or 90 dpf.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol (Life Technologies) according to manufacturer's protocol. To obtain sufficient amount for labelling, whole transcriptome amplification was performed using Ovation RNA Amplificiation System V2 (NuGen).
|
| Label |
Cy3
|
| Label protocol |
Amplified double stranded cDNA was labeled using NimbleGen One-Color DNA Labelling Kit (Roche NimbleGen) according to manufacturer's protocol.
|
| |
|
| Hybridization protocol |
Hybridization was performed for 16 to 20 hours using MAUI hybridization system (BioMicro Systems) according to Roche NimbleGen expression array protocol.
|
| Scan protocol |
Prior to scanning the microarray chip was washed with NimbleGen Wash Buffer Kit (Roche NimbleGen) according to manufacturer's protocol. Then the chip was scanned at 5 um resolution with Axon GenePix 4000B Microarray Scanner (Molecular Devices) according to Roche NimbleGen expression array protocol.
|
| Description |
This sample is a juvenile trunk exposed to control temperature (28 oC). It is fifth of the eight biological replicates.
|
| Data processing |
The raw data(.pair file) was subjected to RMA (Robust-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan version 2.6 software package.
|
| |
|
| Submission date |
Oct 18, 2013 |
| Last update date |
Feb 13, 2017 |
| Contact name |
Woei Chang Liew |
| E-mail(s) |
wcliew@tll.org.sg
|
| Organization name |
Temasek Life Sciences Laboratory
|
| Lab |
Reproductive Genomics
|
| Street address |
1 Research Link, NUS
|
| City |
Singapore |
| ZIP/Postal code |
117604 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL17795 |
| Series (1) |
| GSE51434 |
Zebrafish gonadal transcriptome analysis in response to heat |
|
