|
| Status |
Public on Nov 29, 2011 |
| Title |
Apex TCDD 7 dpa 2 |
| Sample type |
RNA |
| |
|
| Source name |
amputated TCDD 7 dpa rep 2
|
| Organism |
Danio rerio |
| Characteristics |
age: Adult AB
amputated: yes
treatment: TCDD
dpa: 7
|
| Treatment protocol |
Ventricles were removed and separated into two sections: upper (anterior to regenerate; ventricle top) and apex (regenerate and amputation plane; ventricle bottom)
|
| Growth protocol |
Adult zebrafish (danio rerio) were injected (i.p) to vehicle control or TCDD (70 ng/g) one day prior to heart ventricle amputation. A set of fish were not amputated to understand which genes were altered without amputation. Amputated hearts were collected at 6 hours post amputation and 7 days post amputation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using QIAGEN Rneasy Micro Kit. A total of n=10 hearts were pooled per sample.
|
| Label |
Biotin
|
| Label protocol |
cRNA amplification and hybridization was conducted using an Affymetrix GeneChip IVT Express Kit and protocol. 500 ng of total RNA was used to generated cRNA sample.
|
| |
|
| Hybridization protocol |
15 ug of cRNA was hybridized to a zebrafish Affymetrix array for 16 h at 45ºC with rotation (53 rpm). Arrays were washed and stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 400 using protocol EukGE-W32v4.
|
| Scan protocol |
Arrays were scanned using the Agilent gene array scanner (Aligent Technologies, Santa Clara, CA).
|
| Description |
Microarray analysis of 2,3,7,8-Tetrachlorodibenzo-p-dioxin Inhibition of Adult Zebrafish Heart Regeneration
|
| Data processing |
Analysis of microarray data was adapted from Gould et al., 2006. The raw data (.CEL files) were normalized by RMA algorithm using the ExpressionFileCreator module of the Genepattern software. Differences in gene expression by amputation or TCDD exposure were determined using the comparative selection marker module of GenePattern. Cutoffs for statistical significance were a Benjamini- Hochberg corrected False Discovery Rate (FDR) <0.1 and a minimum fold change >2. To compare the change in gene expression induced by amputation in PC or TCDD exposed groups, the log2 values were calculated
|
| |
|
| Submission date |
Nov 28, 2011 |
| Last update date |
Nov 29, 2011 |
| Contact name |
Peter Jacobs Hofsteen |
| E-mail(s) |
phofsteen@wisc.edu
|
| Phone |
608-263-0652
|
| Organization name |
University of Wisconsin - Madison
|
| Department |
Pharmacy
|
| Lab |
Peterson / Heideman
|
| Street address |
777 Highland Ave
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53705 |
| Country |
USA |
| |
|
| Platform ID |
GPL1319 |
| Series (1) |
| GSE33981 |
Microarray analysis of 2,3,7,8-Tetrachlorodibenzo-p-dioxin Exposed Amputated Adult Zebrafish Heart Ventricles |
|
