|
| Status |
Public on Dec 24, 2014 |
| Title |
MODE-K cells_LPS_exo.r2 |
| Sample type |
RNA |
| |
|
| Source name |
MODE-K in medium + LPS + exosomes
|
| Organism |
Mus musculus |
| Characteristics |
cell-line: MODE-K cells
treatment: LPS+exosomes
|
| Treatment protocol |
MODE-K cells were grown in DMEM media as described above and seeded into 24-well plates at 20,000 cells per well. The following day, cells were left untreated or treated with H. polygyrus-derived exosomes (5 ug total protein per well) in DMEM media for 20 hours in the absence or presence of 1 ug/mL LPS, after which cells were washed twice with PBS.
|
| Growth protocol |
MODE-K cells were obtained from Dominique Kaiserlian (INSERM) and grown following standard protocol in DMEM (Invitrogen) medium supplemented with 10% Foetal Bovine Serum (Invitrogen), 1% penicillin-streptomycin (Lonza), 1% L-glutamine (Lonza), 1% non essential amino acids/sodium pyruvate (Gibco).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the miRNAeasy kit.
|
| Label |
biotin
|
| Label protocol |
RNA was prepared for microarray analysis using the Ambion Illumina TotalPrep RNA Amplification kit.
|
| |
|
| Hybridization protocol |
RNA-loaded BeadChips were placed into Hyb Chamber inserts and these were incubated in the Illumina Hybridization Oven for 18 hours at 58°C. BeadChips were then washed as follows: High Temperature wash, 1st Room Temp Wash, Ethanol Wash, 2nd Room Temp Wash, Block with E1 Buffer, *Detect Signal and 3rd Room Temp Wash. BeadChips were then centrifuged immediately to prevent surface evaporation, 1,400rpm at room temperature for 4 minutes.
|
| Scan protocol |
BeadChips were scanned on the iScan System (HiScan H166)
|
| Description |
replicate2
|
| Data processing |
The raw SampleProbeProfile file was processed within R, using ‘lumi’ and ‘lumiMouseAll.db’ Bioconductor packages.Raw expression values were processed with the Variance Stabilizing Transformation and the Robust Spline Normalization. An InterQuartile Range was calculated across all samples for each probe, and used to select the most variable probe of those that mapped to the same transcript. Probes without a gene or transcript annotation were excluded, leaving a total of 30,708 non-redundant annotated probes.
|
| |
|
| Submission date |
Mar 16, 2014 |
| Last update date |
Dec 24, 2014 |
| Contact name |
Cei Abreu-Goodger |
| E-mail(s) |
cei.abreu@cinvestav.mx
|
| Organization name |
Langebio - Cinvestav
|
| Street address |
Km. 9.6 Libramiento Nte Carr Leon-Irapuato
|
| City |
Irapuato |
| State/province |
Guanajuato |
| ZIP/Postal code |
36824 |
| Country |
Mexico |
| |
|
| Platform ID |
GPL6887 |
| Series (1) |
| GSE55941 |
Genome-wide expression analysis of the effects of a parasitic nematode's secreted exosomes on mammalian cells. |
|
