|
| Status |
Public on Dec 06, 2011 |
| Title |
Tbx5 48-2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
zebrafish embryo (tbx5 -MO)
|
| Organism |
Danio rerio |
| Characteristics |
development stage: 48hpf
tissue: whole embryo
strain: AB strain
|
| Treatment protocol |
Isolated total zebrafish embryo RNA was purified using an RNeasy® 257 Mini Kit (QIAGEN, Hilden, Germany)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The quality was confirmed using an Aglient 2100 Bioanalyzer (Aglient Technologies, Santa Cruz, CA, USA). Purified RNA was reverse-transcribed into complementary (c)DNA using SuperScrip TM III RT (Invitrogen, Carlsbad, CA, USA).
|
| Label |
Cy5
|
| Label protocol |
Coupling the fluorescent dye using indirect cDNA labeling with a microarray kit (Invitrogen), the cDNA was hydrolyzed and neutralized using NaOH and HCl.
|
| |
|
| Channel 2 |
| Source name |
zebrafish embryo (Control wilde-type)
|
| Organism |
Danio rerio |
| Characteristics |
development stage: 48hpf
tissue: whole embryo
strain: AB strain
|
| Treatment protocol |
Isolated total zebrafish embryo RNA was purified using an RNeasy® 257 Mini Kit (QIAGEN, Hilden, Germany)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The quality was confirmed using an Aglient 2100 Bioanalyzer (Aglient Technologies, Santa Cruz, CA, USA). Purified RNA was reverse-transcribed into complementary (c)DNA using SuperScrip TM III RT (Invitrogen, Carlsbad, CA, USA).
|
| Label |
Cy3
|
| Label protocol |
Coupling the fluorescent dye using indirect cDNA labeling with a microarray kit (Invitrogen), the cDNA was hydrolyzed and neutralized using NaOH and HCl.
|
| |
|
| |
| Hybridization protocol |
The cDNA was then pretreated with GEx hybridization buffer (HI263 PRM; Aglient Technologies) before transferring to hybridization chamber gasket slides for the hybridization reaction.
|
| Scan protocol |
The slide was scanned with an Axon Instruments GenePix 4000B scanner (Molecular Devices, Silicon Valley, CA, USA)
|
| Data processing |
In our cDNA microarray analysis, the microarray data was normalized by using Genespring 265 GX10.0. software (Aglient Technologies). The MO Tbx5 anti-sense RNA treatment and control (WT) were used in our microarray analsysis. The each sample labeled with Cy5 and Cy3 fluorescent dyes (Amersham Pharmacia Biotech; Piscataway, NJ) and run in paired hybridizations on the arrays. The Lowess normalization was performed after subtracting the median background. Genes with a negative log ratio in green are down-regulated by Tbx5 gene 1.5X knockdown filtered on expression (-10.868 - -0.584) in the normalized data.
|
| |
|
| Submission date |
Nov 28, 2011 |
| Last update date |
Dec 06, 2011 |
| Contact name |
jenn-kan Lu |
| E-mail(s) |
f0008@mail.ntou.edu.tw
|
| Phone |
02-24622192
|
| Fax |
02-24621163
|
| Organization name |
NTOU208
|
| Department |
Aquaculture
|
| Lab |
208
|
| Street address |
2 Pei-Ning Road,Keelung
|
| City |
keelung |
| ZIP/Postal code |
20224 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL6457 |
| Series (1) |
| GSE33965 |
Danio rerio: wilde-type control vs. tbx5 morpholino |
|
