|
| Status |
Public on Feb 17, 2006 |
| Title |
C57BL/6 vs. C57BL/6 Cholesterol H.pylori |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
C57BL/6
|
| Organism |
Mus musculus |
| Characteristics |
Female C57BL/6 mice (6 weeks old, Charles River, Sulzfeld, Germany). The stomach was removed, and the stomach mucosa was scraped off with a sterile scalpel blade on liquid nitrogen until ~2/3 of the tissue was removed.
|
| Extracted molecule |
total RNA |
| Label |
Cy3
|
| |
|
| Channel 2 |
| Source name |
C57BL/6 Cholesterol H.pylori
|
| Organism |
Mus musculus |
| Characteristics |
Female C57BL/6 mice (6 weeks old, Charles River, Sulzfeld, Germany) were infected with a single oral dose of 9.5 × 10e8 Hp76 cells suspended in PBS and 0.2 M NaHCO3. The stomach was removed, and the stomach mucosa was scraped off with a sterile scalpel blade on liquid nitrogen until ~2/3 of the tissue was removed.
|
| Extracted molecule |
total RNA |
| Label |
Cy5
|
| |
|
| |
| Description |
Total RNA was prepared using the RNeasy protocol with on-column DNAse digestion (Qiagen, Hilden, Germany) and confirmed to be intact and free of contaminating DNA using an Agilent 2100 bioanalyzer and a RNA 6000 Nano LabChip kit (Agilent Technologies, Palo Alto, CA). A custom tailored 'in situ' synthesized 60-mer oligonucleotide microarray (Agilent) comprising 8014 murine genes with immunological focus was used for expression profiling. RNA was amplified and labeled using a reverse-transcriptase/T7 polymerase linear amplification labeling kit (Agilent), and 1.5 mg of respective cRNAs labeled either with Cy3 or Cy5 were hybridized for 16 h at 65°C. Slides were used and processed according to the manufacturer's manuals.
|
| Data processing |
Features were extracted with an Image Analysis software (Version A.7.5.1, Agilent). Intensities were normalized by local background correction and by rank consistency filtering with a combination of linear and LOWESS normalization. Data analysis was performed with Rosetta Resolver Biosoftware (Build 5.1.0.0.163, Rosetta Biosoftware, Seattle, WA).
|
| |
|
| Submission date |
Feb 16, 2006 |
| Last update date |
Feb 17, 2006 |
| Contact name |
Hans-Joachim Mollenkopf |
| E-mail(s) |
mollenkopf@mpiib-berlin.mpg.de
|
| Phone |
+49 30 28460 482
|
| Organization name |
Max-Planck-Institute for Infection Biology
|
| Lab |
Microarray/Genomics Core Facility
|
| Street address |
Charitéplatz 1
|
| City |
Berlin |
| ZIP/Postal code |
10117 |
| Country |
Germany |
| |
|
| Platform ID |
GPL1868 |
| Series (1) |
| GSE3878 |
Sugar turns benefit of cholesterol into immune evasion in Helicobacter pylori infected C57BL/6 mice |
|
