|
| Status |
Public on Dec 22, 2010 |
| Title |
iNOS d60 lung vs. iNOS d60 aIFNg lung |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
iNOS d60 lung
|
| Organism |
Mus musculus |
| Characteristics |
strain: NOS2-/- knock-out (iNOS)
|
| Treatment protocol |
The ear dermis of NOS2-/- knock-out (iNOS) mice was infected with 1e+4 c.f.u. Mtb in a volume of 10 µl. Mice were sacrificed at day 60 and lungs were removed aseptically for total RNA preparation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen) using Glycogen as carrier.
|
| Label |
cy3
|
| Label protocol |
RNA labeling was performed with the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). In brief, mRNA was reverse transcribed and amplified using an oligo-dT-T7-promotor primer and resulting cRNA was labeled either with Cyanine 3-CTP.
|
| |
|
| Channel 2 |
| Source name |
iNOS d60 aIFNg lung
|
| Organism |
Mus musculus |
| Characteristics |
strain: NOS2-/- knock-out (iNOS)
|
| Treatment protocol |
The ear dermis of NOS2-/- knock-out (iNOS) mice was infected with 1e+4 c.f.u. Mtb in a volume of 10 µl. For antibody treatment, dermal infected mice were administered 500 µg XMG1.2 (ATCC) (anti-interferon gamma, aIFNg) in PBS intraperitoneally on day 7 and day 14 post infection.Mice were sacrificed at day 60 and lungs were removed aseptically for total RNA preparation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen) using Glycogen as carrier.
|
| Label |
Cy5
|
| Label protocol |
RNA labeling was performed with the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). In brief, mRNA was reverse transcribed and amplified using an oligo-dT-T7-promotor primer and resulting cRNA was labeled either with Cyanine 5-CTP.
|
| |
|
| |
| Hybridization protocol |
Whole mouse genome 44k microarrays were done according to the supplier’s protocol (Agilent Technologies) using the SSC wash protocol Version 4.1
|
| Scan protocol |
Scanning of microarrays was performed with 5 µm resolution using a DNA microarray laser scanner (Agilent Technologies) and default settings (GE2-v4_95_Feb07).
|
| Description |
Microarray experiments were performed as dual-color hybridizations. To compensate for dye-specific effects, a dye-reversal color-swap was applied.
|
| Data processing |
Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.9.5.1, Agilent). The extracted MAGE-ML files were analyzed with the Rosetta Resolver Biosoftware, Build 6.1 (Rosetta Biosoftware).
|
| |
|
| Submission date |
Feb 13, 2009 |
| Last update date |
Dec 22, 2010 |
| 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 |
GPL2872 |
| Series (1) |
| GSE14826 |
A serine protease inhibitor induces necrosis of infected macrophages within granulomas during activation of tuberculosis |
|
