|
| Status |
Public on Apr 30, 2012 |
| Title |
9h amputated runt-1 RNAi animals (replicates 1-3) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
runt-1(RNAi) animals
|
| Organism |
Schmidtea mediterranea |
| Characteristics |
tissue type: clone W4, asexual
|
| Treatment protocol |
Animals were fed respective RNAi food (bacteria expressing dsRNA of gene of interest mixed with homogenized calf liver) every 4 days for 12 days.
|
| Growth protocol |
Clone W4 Schmidtea mediterranea were kept at 20degree Celsius in Monbijou Salts
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted 5 days following the last feeding using TRIZOL according to manufacterer's instructions
|
| Label |
Cy5
|
| Label protocol |
RNA was labeled using Agilent's two-color QuickAmp labeling kit
|
| |
|
| Channel 2 |
| Source name |
unc-22(RNAi) animals
|
| Organism |
Schmidtea mediterranea |
| Characteristics |
tissue type: clone W4, asexual
|
| Treatment protocol |
Animals were fed respective RNAi food (bacteria expressing dsRNA of gene of interest mixed with homogenized calf liver) every 4 days for 12 days.
|
| Growth protocol |
Clone W4 Schmidtea mediterranea were kept at 20degree Celsius in Monbijou Salts
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted 5 days following the last feeding using TRIZOL according to manufacterer's instructions
|
| Label |
Cy3
|
| Label protocol |
RNA was labeled using Agilent's two-color QuickAmp labeling kit
|
| |
|
| |
| Hybridization protocol |
Agilent DNA microarray scanner
|
| Scan protocol |
Agilent’s Feature Extraction Image Analysis software with the default two-color gene expression protocol
|
| Description |
Biological replicas 1 - 3 combined for analysis. RNAi animals harvested 9h after amputation
|
| Data processing |
Agilent two-color arrays were within-array normalized by loess, followed by between-array quantile normalization of average intensities across channels (Aquantile). Differential expression analysis was performed using a moderated t-test, as implemented in the limma package of Bioconductor, with P-value correction by false discovery rate.
|
| |
|
| Submission date |
Mar 28, 2012 |
| Last update date |
Apr 30, 2012 |
| Contact name |
Danielle Wenemoser |
| E-mail(s) |
wenemoser@wi.mit.edu
|
| Phone |
617-324-2147
|
| Organization name |
Whitehead Institute for Biomedical Research
|
| Lab |
Reddien Lab
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL14150 |
| Series (1) |
| GSE36869 |
Transcriptional profiling of Schmidtea mediterranea planarians (smed-runt-1 RNAi vs. control RNAi) |
|
