|
| Status |
Public on Dec 27, 2011 |
| Title |
Hybrid_Strain_Female8 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Hybrid Strain Adult, Whole animal homogenate
|
| Organism |
Danio rerio |
| Characteristics |
sample type: Hybrid Strain (AB x unknown)
|
| Growth protocol |
Laboratory animals were raised using standard IACUC approved methods. Native fish were captured and shipped from Bangladesh to the University of Exeter where they were raised using standarad approved culture methods
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol simultaneous extraction of DNA and RNA
|
| Label |
Cy3
|
| Label protocol |
Samples were labeled using the standard Agilent array CGH protocol with the following modifications: our experiments used 1 ug of heat denatured DNA (5 minutes at 95°C) per labeling reaction in place of the 1 ug of restriction enzyme-digested DNA, as indicated in the standard protocol. Reference samples were labeled with Cy3-dCTP and Test Samples were labeled with Cy5-dCTP.
|
| |
|
| Channel 2 |
| Source name |
Hybrid Female8, Whole Animal Homogenate
|
| Organism |
Danio rerio |
| Characteristics |
sample type: Hybrid Strain (AB x unknown)
|
| Growth protocol |
Laboratory animals were raised using standard IACUC approved methods. Native fish were captured and shipped from Bangladesh to the University of Exeter where they were raised using standarad approved culture methods
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol simultaneous extraction of DNA and RNA
|
| Label |
Cy5
|
| Label protocol |
Samples were labeled using the standard Agilent array CGH protocol with the following modifications: our experiments used 1 ug of heat denatured DNA (5 minutes at 95°C) per labeling reaction in place of the 1 ug of restriction enzyme-digested DNA, as indicated in the standard protocol. Reference samples were labeled with Cy3-dCTP and Test Samples were labeled with Cy5-dCTP.
|
| |
|
| |
| Hybridization protocol |
Labeled Reference and Test samples were combined with hybridization buffer, as described in the standard Agilent protocol, and applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential in Buffer 1 and Buffer 2. Buffere 3 was not used as the scanner is in an ozone hood.
|
| Scan protocol |
Scanned on an Agilent G2505C scanner. At 2 micorns.
|
| Description |
Hybrid Reference vs. Hybrid Female8
|
| Data processing |
Normalized, background subtracted data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.
|
| |
|
| Submission date |
Mar 29, 2011 |
| Last update date |
Dec 27, 2011 |
| Contact name |
Charles Lee |
| E-mail(s) |
clee@rics.bwh.harvard.edu
|
| Organization name |
Brigham and Women's Hospital/Harvard Medical School
|
| Department |
Pathology
|
| Lab |
Lee Lab--Molecular Genetic Research Unit
|
| Street address |
221 Longwood Ave., EBRC-422
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL6457 |
| Series (2) |
| GSE28239 |
Identification and functional impact of genomic copy number variants in zebrafish, an important human disease model (Zebrafish Strain CNVs) (expression array) |
| GSE28328 |
Extensive genetic diversity and substructuring among zebrafish strains revealed through copy number variant analysis |
|
