|
| Status |
Public on Jul 25, 2015 |
| Title |
M7_vs_WT7_rep1_dye_swap |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
caecum
|
| Organism |
Mus musculus |
| Characteristics |
tissue: caecum
strain: C57BL6J
genotype: infected Nlrp12-/-
treatment: day 7
|
| Treatment protocol |
Nlrp12-deficient and wild type C57BL6/J mice were infected or not with 1x10^9 colony-forming units of C. rodentium
|
| Growth protocol |
RNA was isolated from the caecum of Nlrp12-deficient and wild type mice at day 0 and 7 post C. rodentium infection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Rneasy Mini kit- Qiagen following manufacturer's instructions
|
| Label |
cy3
|
| Label protocol |
500 ng of total RNA were labeled using Quick-amp labeling kit 2 colors, following manufacturer's informations
|
| |
|
| Channel 2 |
| Source name |
caecum
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6J
tissue: caecum
genotype: infected wild-type
treatment: day 7
|
| Treatment protocol |
Nlrp12-deficient and wild type C57BL6/J mice were infected or not with 1x10^9 colony-forming units of C. rodentium
|
| Growth protocol |
RNA was isolated from the caecum of Nlrp12-deficient and wild type mice at day 0 and 7 post C. rodentium infection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Rneasy Mini kit- Qiagen following manufacturer's instructions
|
| Label |
cy5
|
| Label protocol |
500 ng of total RNA were labeled using Quick-amp labeling kit 2 colors, following manufacturer's informations
|
| |
|
| |
| Hybridization protocol |
850 ng of each linearly amplified cRNA per cyanine were cohybridized on microarrays ( Agilent-014868 Whole Mouse Genome Microarray 4x44K G4122F) using Agilent Gene Expression Hybridization Kit , and enclosed in Agilent SureHyb-enabled hybridization chambers during 17 hours at 65°C rotated at 10 rpm . After hybridization, slides were washed sequential
|
| Scan protocol |
Scanned on an Innoscan 700 scanner ( Innopsys )
Images were quantified using Mapix Software (version 3.2.1).
|
| Description |
C rodentium infected Nlrp12-deficient C57BL6J mouse at day 7 (test) versus C rodentium infected Wild-type mouse at day 7 replicate 1 by dye swap color (reference)
Biological replicate 1 of 3
In the sample table, the dye-swap sample values have been inversed, so that all table values display test over reference.
|
| Data processing |
A specific script on R was used ( limma library ) for LOWESS normalization within slide and between slides.
|
| |
|
| Submission date |
Jul 30, 2014 |
| Last update date |
Jul 25, 2015 |
| Contact name |
Mathias Chamaillard |
| E-mail(s) |
mathias.chamaillard@inserm.fr
|
| Organization name |
Inserm
|
| Department |
Center for Infection and Immunity of Lille
|
| Lab |
Nods-like receptors in infection and immunity
|
| Street address |
1, rue Prof A. Calmette
|
| City |
Lille |
| ZIP/Postal code |
59019 |
| Country |
France |
| |
|
| Platform ID |
GPL7202 |
| Series (1) |
| GSE59940 |
The Nlrp12 inflammasome negatively regulates NOD2-mediated adjuvanticity, endotoxic shock and host defence afforded by an immunomodulatory muropeptide. |
|
