|
| Status |
Public on Jul 01, 2013 |
| Title |
whole_time1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Upf2-25G/Y mutant
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype/variation: Upf2-25G/Y mutant
tissue: whole animal
treatment: 2 hour after heatshock
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole animals or cells were homogenized in Trizol (Invitrogen, Carlsbad, CA) and total RNA extracted using a standard three phase chloroform technique (Chomczynski and Sacchi 1987). RNA was purified and concentrated using the RNeasy column (Qiagen Inc., Maryland), including an on-column treatment with DNase I. Random decamer-primed cDNA was prepared using M-MLV reverse transcriptase (RNase H+) as part of the RERTOscript kit (Ambion, Austin, TX).
|
| Label |
Cy3
|
| Label protocol |
Labeled cRNA was generated by incorporating cyanine 3-CTP or cyanine 5-CTP into a T7 RNA polymerase reaction using the cDNA as template.
|
| |
|
| Channel 2 |
| Source name |
Upf2-25G/Y mutant with UAS:Upf2
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype/variation: Upf2-25G/Y mutant with UAS:Upf2
tissue: whole animal
treatment: 2 hour after heatshock
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole animals or cells were homogenized in Trizol (Invitrogen, Carlsbad, CA) and total RNA extracted using a standard three phase chloroform technique (Chomczynski and Sacchi 1987). RNA was purified and concentrated using the RNeasy column (Qiagen Inc., Maryland), including an on-column treatment with DNase I. Random decamer-primed cDNA was prepared using M-MLV reverse transcriptase (RNase H+) as part of the RERTOscript kit (Ambion, Austin, TX).
|
| Label |
Cy5
|
| Label protocol |
Labeled cRNA was generated by incorporating cyanine 3-CTP or cyanine 5-CTP into a T7 RNA polymerase reaction using the cDNA as template.
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed on an Agilent Drosophila 44K array using a Agilent SureHyb hybridization oven.
|
| Scan protocol |
Hybridized chips were scanned using a Agilent G2505C Microarray Scanner and signal processing accomplished with Agilent Feature Extraction software, v 10.5.
|
| Data processing |
The Limma package in R (Smyth and Speed 2003) was used to perform background correction and loess normalization.
|
| |
|
| Submission date |
Jun 14, 2013 |
| Last update date |
Jul 01, 2013 |
| Contact name |
Hao Hu |
| Organization name |
MD Anderson Cancer Center
|
| Department |
Epidemiology
|
| Lab |
Huff lab
|
| Street address |
1155 Pressler Blvd, Unit 1340
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL7300 |
| Series (1) |
| GSE47979 |
In vivo determination of candidate direct targets of the nonsense mediated decay pathway in intact Drosophila |
|
