|
| Status |
Public on Oct 12, 2015 |
| Title |
BMN_FS2_MoGene |
| Sample type |
RNA |
| |
|
| Source name |
LC.Epidermis
|
| Organism |
Mus musculus |
| Characteristics |
cell population: CD11b+MHCII+CD24+
cell type: Epidermal Langerhans Cells
treatment: Untreated
|
| Treatment protocol |
Mice at 8 to 11 weeks of age received on a daily basis and for 14 consecutive days a dose of 5 % IMQ cream (Aldara, MEDA Pharma, Paris, France) applied topically on the ear skin and corresponding to 7 mg IMQ per ear side
|
| Growth protocol |
To extract skin mononuclear phagocytic cells, ears were splitted into dorsal and ventral parts and incubated with a solution of PBS containing 1 mg/mL dispase (Roche) for 2 h at 37° C or overnight at 4° C, as specified. The dorsal and ventral parts were then cut into small pieces and incubated for 90 min at 37° C with RPMI containing 1 mg/mL DNase and 1 mg/mL Collagenase IV (Worthington Biochemical). The resulting single cell suspension was subjected to centrifugation on a Percoll gradient (Amersham-Pharmacia).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Each cell subset was purified by flow cytometry and total RNA was extracted with the Qiagen micro RNAeasy kit, with on column DNase digestion, according to the manufacturer protocol.
|
| Label |
biotin
|
| Label protocol |
1 to 20 ng of RNA from each sample was used to synthesize biotinylated probes, using 2 successive rounds of cRNA amplification (using the NuGEN Ovation Pico WTA System V2 Kit and the NuGEN Encore Biotin Module Kit according to NuGEN recommendations) with appropriate quality control to ensure full length synthesis.
|
| |
|
| Hybridization protocol |
Following fragmentation and end-labeling, 2.07 μg of cDNAs were hybridized for 16 hours at 45°C on Affymetrix GeneChip Mouse Gene 1.0 ST arrays. The chips were washed and stained in the GeneChip Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.
|
| Data processing |
The data were RMA normalized in R and Bioconductor, using the oligo package. Two matrices was generated. Matrix1 corresponds to all probesets. Matrix2 corresponds to probes showing a fold change ≥2 and a p-value <0.05 for at least one cell type between D5 or D11 versus D0 using the LIMMA statistical package of the R program.
|
| |
|
| Submission date |
Jan 26, 2015 |
| Last update date |
Oct 23, 2015 |
| Contact name |
Marc DALOD |
| E-mail(s) |
dalod@ciml.univ-mrs.fr
|
| Organization name |
CIML
|
| Street address |
Parc Scientifique et Technologique de Luminy, 163 avenue de Luminy, Case 906, 13288 Marseille cedex 9
|
| City |
MARSEILLE |
| ZIP/Postal code |
13009 |
| Country |
France |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE65309 |
Proliferating Langerhans cells dampen inflammation in established mouse psoriatic lesions |
|
| Relations |
| Reanalyzed by |
GSE74316 |
