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Status |
Public on Apr 03, 2018 |
Title |
Patient_1_-D-LP, biological replicate 1 |
Sample type |
RNA |
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Source name |
PBMCs by density-gradient centrifugation
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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.
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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).
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Hybridization protocol |
Hybridization was performed for 16 hours at 45 degrees celsius using the GeneChip Hybridization Oven 645 (Affymetrix, St. Clara, USA).
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Scan protocol |
Scanning was done using the GeneChip Scanner 3000/7G (Affymetrix, St. Clara, USA) with 0.7 micron resolution.
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Description |
Gene expression data of patient
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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)
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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 |
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