|
| Status |
Public on Apr 28, 2023 |
| Title |
RafGOFscirb- tumor at Day10, biological rep2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Drosophila tumors from third instar larvae
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: eye-antennal discs at 3rd instar larval stage (Day 10)
|
| Growth protocol |
Flies were raised on standard Drosophila media at 25°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Approximately 30-40 discs were dissected from third instar larvae (wild-type, day 5-6 AEL; tumors, day 10 AEL) and placed in 300 μl TRIzol (Invitrogen) to isolate total RNAs.
|
| Label |
Cy3
|
| Label protocol |
mRNA amplification and labeling were performed with random hexamers as previously reported (Baugh et al., 2001). Wild-type reference mRNAs were labeled with dUTP-Cy5 and tumor mRNAs with dUTP-Cy3.
|
| |
|
| Channel 2 |
| Source name |
Drosophila wild-type reference from third instar larvae
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissues: eye-antennal discs at 3rd instar stage (Day5-6)
|
| Growth protocol |
Flies were raised on standard Drosophila media at 25°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Approximately 30-40 discs were dissected from third instar larvae (wild-type, day 5-6 AEL; tumors, day 10 AEL) and placed in 300 μl TRIzol (Invitrogen) to isolate total RNAs.
|
| Label |
Cy5
|
| Label protocol |
mRNA amplification and labeling were performed with random hexamers as previously reported (Baugh et al., 2001). Wild-type reference mRNAs were labeled with dUTP-Cy5 and tumor mRNAs with dUTP-Cy3.
|
| |
|
| |
| Hybridization protocol |
Reference and tumor mRNAs were hybridized to custom-made slides using a solution of TE, SSC, SDS and poly-A as a blocking agent. Hybridization was performed in chambers (DIE-TECH) for 10 min at 42°C, then approximately 15 hours at 64°C. Slides were washed three times with increasingly dilute concentrations of SSC, then dried.
|
| Scan protocol |
Images were scanned on an Axon 4000B scanner and analyzed using GenePix Pro 3.0 software (Axon Instruments).
|
| Data processing |
The raw measurements produced were the median fluorescence of each spot for the wavelength of the reference and tumor sample, as well as the ratio of Medians. These data were further lowess normalized and analyzed using GeneSpring software (Silicon Genetics).
|
| |
|
| Submission date |
Jun 08, 2016 |
| Last update date |
Apr 28, 2023 |
| Contact name |
Tian Xu |
| E-mail(s) |
tian.xu@yale.edu
|
| Organization name |
Yale school of medicine
|
| Department |
Genetics
|
| Lab |
Tian Xu's Lab
|
| Street address |
295 congress ave
|
| City |
new haven |
| State/province |
CONNECTICUT |
| ZIP/Postal code |
06519 |
| Country |
USA |
| |
|
| Platform ID |
GPL21995 |
| Series (1) |
| GSE83119 |
Expression data of Drosophila malignant tumors of distinct genetic orgins |
|
