|
| Status |
Public on Mar 28, 2017 |
| Title |
2008124 4.08 48 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
whole brain
|
| Organism |
Xenotilapia ochrogenys |
| Characteristics |
Sex: male
mating type: monogamous
ID: Xo110
|
| Treatment protocol |
brains were extracted from animals captured in the wild. Animals were euthanized as quickly as possible after capture and brains were rapidly removed and stored in RNAlater solution.
|
| Growth protocol |
adult
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with standard trizol protocol
|
| Label |
Cy3
|
| Label protocol |
2µg of total RNA from whole brain was reverse transcribed and labeled according to Renn et al. (2004): Briefly, amino-allyl dUTP (Sigma) was incorporated to the cDNA using oligo-dT(12 -18) with SuperScript II (Invitrogen) according to the manufacturer’s protocol, dye-coupling with Cy3 or Cy5 (CyDye Post-Labeling Reactive Dye Pack, Amersham) following RNA hydrolyzation and purification.
|
| |
|
| Channel 2 |
| Source name |
whole brain
|
| Organism |
Xenotilapia tenuidentata |
| Characteristics |
Sex: male
mating type: polygynous
ID: Mt105
|
| Treatment protocol |
brains were extracted from animals captured in the wild. Animals were euthanized as quickly as possible after capture and brains were rapidly removed and stored in RNAlater solution.
|
| Growth protocol |
adult
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with standard trizol protocol
|
| Label |
cy5
|
| Label protocol |
2µg of total RNA from whole brain was reverse transcribed and labeled according to Renn et al. (2004): Briefly, amino-allyl dUTP (Sigma) was incorporated to the cDNA using oligo-dT(12 -18) with SuperScript II (Invitrogen) according to the manufacturer’s protocol, dye-coupling with Cy3 or Cy5 (CyDye Post-Labeling Reactive Dye Pack, Amersham) following RNA hydrolyzation and purification.
|
| |
|
| |
| Hybridization protocol |
The neutralized color reaction was purified and combined with the appropriate competitive sample in hybridization buffer containing SSC and HEPES buffer with poly(dA)-poly(dT) (Sigma) for blocking and 0.1% for overnight hybridization at 65º C.
|
| Scan protocol |
After hybridization arrays were scanned (Axon 4000B: Axon Instruments) using Genepix 5.0 software (Axon Instruments) matching laser power and PMT to roughly normalize the two chanels.
|
| Data processing |
Data were filtered for feature quality and diameter, high background intensity, and low feature intensity. Features with demonstrated effects of sequence divergence (poor gDNA hybridization) were also filtered out.
|
| |
|
| Submission date |
Mar 27, 2017 |
| Last update date |
Mar 28, 2017 |
| Contact name |
Suzy C.P. Renn |
| E-mail(s) |
renns@reed.edu
|
| Phone |
503 517 7967
|
| Organization name |
Reed College
|
| Department |
Biology
|
| Street address |
3203 SE Woodstock Blvd
|
| City |
Portland |
| State/province |
OR |
| ZIP/Postal code |
97202 |
| Country |
USA |
| |
|
| Platform ID |
GPL6416 |
| Series (1) |
| GSE97082 |
Ectodini cichlid brain comparison of mating type |
|
