|
| Status |
Public on Mar 08, 2010 |
| Title |
brain replicate1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
common reference
|
| Organism |
Gallus gallus |
| Characteristics |
strain: Lohmann Brown
sample: pooled common reference from individual tissues
age: 10 wk
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions, followed by a subsequent sample clean-up using Rneasy Mini Kit (Qiagene).
|
| Label |
Cy5
|
| Label protocol |
RNA was amplified using MessageAmp II aRNA kit (Ambion), cRNA was further used for chemical coupling with ULS-Cy3/Cy5 (ULS aRNA labeling kit, Kreatech, Amsterdam, the Netherlands).
|
| |
|
| Channel 2 |
| Source name |
brain
|
| Organism |
Gallus gallus |
| Characteristics |
strain: Lohmann Brown
tissue: brain
age: 10 wk
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions, followed by a subsequent sample clean-up using Rneasy Mini Kit (Qiagene).
|
| Label |
Cy3
|
| Label protocol |
RNA was amplified using MessageAmp II aRNA kit (Ambion), cRNA was further used for chemical coupling with ULS-Cy3/Cy5 (ULS aRNA labeling kit, Kreatech, Amsterdam, the Netherlands).
|
| |
|
| |
| Hybridization protocol |
1 ug of labeled cRAN was used to hybridize on the chicken 20k oligo array overnight on a GeneTAC hybridization station (Genomic Solutions)
|
| Scan protocol |
Scanned on an Agilent DNA microarray scanner.
Images were quantified using GenePix Pro 5.0 (Axon).
|
| Description |
biological replicate 1 of 5, normal brain tissue
|
| Data processing |
median values of both foreground and background intensities were used, raw data were further analyzed using R package limma, background was corrected using normexp+offset(50), printtip loess normalized within array, Rquantile normalized among arrays.
|
| |
|
| Submission date |
Jul 15, 2009 |
| Last update date |
Feb 09, 2010 |
| Contact name |
Haisheng Nie |
| E-mail(s) |
Hsh.Nie@gmail.com
|
| Phone |
+31 317 483397
|
| Fax |
+31 317 483929
|
| URL |
http://www.abg.wur.nl/uk
|
| Organization name |
Wageningen University
|
| Lab |
Animal Breeding and Genomic Centre
|
| Street address |
Marijkeweg 40
|
| City |
Wageningen |
| ZIP/Postal code |
6709 PG |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL8861 |
| Series (1) |
| GSE17108 |
A survey of gene expression in adult chicken tissues using a chicken 20K oligonucleotide microarray |
|
