|
| Status |
Public on Jan 29, 2012 |
| Title |
intestine_group6_8hpi_chick6 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
jejunum, group 6, 8 hours pi
|
| Organism |
Gallus gallus |
| Characteristics |
infection: Salmonella
tissue: intestine
group: 6
age: 8h
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen jejunum samples were homogenized in liquid nitrogen using a mortar and pestle. 50-100 mg of the homogenized tissue samples were dissolved in 1 ml of TRIzol reagent (Invitrogen, Breda, The Netherlands) using a syringe and 21-G needle passing the lysate for 10 times. After centrifugation the supernatant was transferred to a fresh tube and phase separation with chloroform was performed. The RNA was precipitated using 500 μl 2-propanol and used for microarray analysis.
|
| Label |
Cy5
|
| Label protocol |
Total RNA (5 μg) was labeled using the MICROMAX TSA labeling and detection kit (PerkinElmer, Wellesley, MA, USA) according to suppliers instruction with minor modifications as described by Van Hemert et al. (van Hemert et al., 2007).
|
| |
|
| Channel 2 |
| Source name |
total RNA from pooled intestine all samples
|
| Organism |
Gallus gallus |
| Characteristics |
tissue: intestine
reference: RNA reference pool (from pooled intestine all samples)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen jejunum samples were homogenized in liquid nitrogen using a mortar and pestle. 50-100 mg of the homogenized tissue samples were dissolved in 1 ml of TRIzol reagent (Invitrogen, Breda, The Netherlands) using a syringe and 21-G needle passing the lysate for 10 times. After centrifugation the supernatant was transferred to a fresh tube and phase separation with chloroform was performed. The RNA was precipitated using 500 μl 2-propanol and used for microarray analysis.
|
| Label |
Cy3
|
| Label protocol |
Total RNA (5 μg) was labeled using the MICROMAX TSA labeling and detection kit (PerkinElmer, Wellesley, MA, USA) according to suppliers instruction with minor modifications as described by Van Hemert et al. (van Hemert et al., 2007).
|
| |
|
| |
| Hybridization protocol |
Total RNA (5 μg) was hybridized using the MICROMAX TSA labeling and detection kit (PerkinElmer, Wellesley, MA, USA) according to suppliers instruction with minor modifications as described by Van Hemert et al. (van Hemert et al., 2007).
|
| Scan protocol |
After signal amplification, the microarrays were dried and scanned for Cy5 and Cy3 fluorescence intensities using a Axon GenePix® Microarray Scanner and GenePix Pro 6.1 software (Molecular Devices, Sunnyvale, CA, USA).
|
| Description |
intestine_group6_8hpi_chick6
|
| Data processing |
Bioconductor limma package was used, background correction with normexp, data was log2-transformed, loess normalized (within arrays) and quantile normalized (between arrays)
|
| |
|
| Submission date |
Feb 04, 2011 |
| Last update date |
Jan 29, 2012 |
| Contact name |
Dirkjan Schokker |
| E-mail(s) |
dirkjan.schokker@wur.nl
|
| Organization name |
Wageningen UR
|
| Department |
Wageningen Livestock Research
|
| Street address |
Droevendaalsesteeg 1
|
| City |
Wageningen |
| ZIP/Postal code |
6708 PB |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL5480 |
| Series (1) |
| GSE27069 |
Gene expression in three different chicken lines after Salmonella infection early in life |
|
