|
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) |
|