|
| Status |
Public on Apr 03, 2018 |
| Title |
Patient_3_-D-LP, biological replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
PBMCs by density-gradient centrifugation
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: PBMC
disease state: Crohn’s disease
treatment: none
|
| Treatment protocol |
1α,25-dihydroxyvitamin D3 (Santa Cruz Biotechnology, Dallas, Texas, USA) at 40 nM was used for an incubation period of 20 h at 37 °C in a 5 % CO2 humidified atmosphere. Lipopolysaccharide (LPS; 1 μg/ml; Sigma-Aldrich, Deisenhofen, Germany) and peptidoglycan (PGN; 10 μg/ml; Sigma-Aldrich) were added to the cells and incubated for another 6 h.
|
| Growth protocol |
After thawing, the cells were cultured in RPMI-1640 medium supplemented with 10 % FCS and 1 % penicillin/streptomycin (all reagents from Biochrom/Merck, Berlin, Germany).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Plus kit (Qiagen, Hilden, Germany) according to the manufacturer`s instruction.
|
| Label |
biotin
|
| Label protocol |
200 ng total RNA was labeled using WT-labeling protocol (Affymetrix/Thermofisher).
|
| |
|
| Hybridization protocol |
Hybridization was performed for 16 hours at 45 degrees celsius using the GeneChip Hybridization Oven 645 (Affymetrix, St. Clara, USA).
|
| Scan protocol |
Scanning was done using the GeneChip Scanner 3000/7G (Affymetrix, St. Clara, USA) with 0.7 micron resolution.
|
| Description |
Gene expression data of patient
|
| Data processing |
Data were processed by SST-RMA (signal space transformation with robust multichip averaging) using TAC 4.0 (transcriptome analysis console 4.0, Applied Biosystems)
|
| |
|
| Submission date |
Feb 06, 2018 |
| Last update date |
Apr 03, 2018 |
| Contact name |
Dirk Koczan |
| E-mail(s) |
dirk.koczan@med.uni-rostock.de
|
| Phone |
+493814945885
|
| Organization name |
University of Rostock
|
| Department |
Institute for Immunology
|
| Street address |
Schillingallee 70
|
| City |
Rostock |
| ZIP/Postal code |
18057 |
| Country |
Germany |
| |
|
| Platform ID |
GPL23159 |
| Series (1) |
| GSE110186 |
NOD2- and disease-specific gene expression profiles of peripheral blood mononuclear cells from Crohn’s disease patients |
|
