|
| Status |
Public on Apr 04, 2024 |
| Title |
Finnish_healthy_3515 |
| Sample type |
RNA |
| |
|
| Source name |
PBMC
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
nationality: Finnish
diagnosis: healthy
|
| Treatment protocol |
PBMCs were extracted from the blood by CPT tubes.
|
| Growth protocol |
Cells were incubated at +37 °C incubator at 5% CO2 for 24 hours in complete RPMI.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from 1x106 PBMCs by AllPrep DNA/RNA Universal Kit (Qiagen). Quantity of the samples were determined by NanoDrop spectrophotometer and Qubit fluorometere, and quality by Agilent Bioanalyzer 2100. Samples with RNA integrity number > 8 were selected and independent pools of two RNA samples were used for the analysis.
|
| Label |
Cy3
|
| Label protocol |
Samples were amplified using T7 RNA polymerase method and the cRNAs were further labeled with Cy3 and Cy5 dye, according to the manufacturer's recommendations.
|
| |
|
| Hybridization protocol |
Labeled cRNAs were hybridized to Agilent 2-color 60-mer oligo arrays according to the manufacturer's recommendations.
|
| Scan protocol |
Slides were washed and scanned with Agilent Microarray scanner G2505C, according to the manufacturer's recommendations.
|
| Description |
Study subject, 3515_F cell sample
|
| Data processing |
Raw intensity values were obtained from Agilent Feature Extraction software and quality checked according to Agilent standard procedures. The median foreground intensities were imported into eUtopia bioinformatics package and analyzed with BioConductor package Limma. Data was quantile normalized based on cutoff 0.75 and percentage of samples 50%. Replicate control probes were combined by their median values.
Log2 transformation and quantile normalization.
|
| |
|
| Submission date |
Apr 04, 2022 |
| Last update date |
Apr 04, 2024 |
| Contact name |
Piia Karisola |
| E-mail(s) |
piia.karisola@helsinki.fi
|
| Phone |
+358503635136
|
| Organization name |
University of Helsinki
|
| Department |
Medical Faculty, Human Microbes Research Program Unit
|
| Street address |
Haartmaninkatu 3
|
| City |
Helsinki |
| State/province |
Southern Finland |
| ZIP/Postal code |
00290 |
| Country |
Finland |
| |
|
| Platform ID |
GPL20844 |
| Series (1) |
| GSE200158 |
Epigenetic differences in long non-coding RNA expression in Finnish and Russian Karelia teenagers with contrasting risk of allergy and asthma |
|
