|
Status |
Public on Mar 28, 2017 |
Title |
2008125 4.08 56 |
Sample type |
RNA |
|
|
Channel 1 |
Source name |
whole brain
|
Organism |
Xenotilapia tenuidentata |
Characteristics |
Sex: male mating type: polygynous ID: Mt101
|
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 leptura |
Characteristics |
Sex: male mating type: monogamous ID: Al109
|
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 |
|