|
| Status |
Public on Nov 06, 2018 |
| Title |
WBS_074_08_06 |
| Sample type |
RNA |
| |
|
| Source name |
Peripheral blood from WBS patient
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: Williams Syndrome (WS)
tissue: whole blood
age: 10y
gender: male
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from peripheral blood of participants by using the Paxgene Blood RNA System (QIAGEN, Tokyo, Japan) following the manufacture’s protocol with on-column DNase digestion.RNA quantity was measured using a Nano-drop ND-2000 spectrophotometer (Thermo Fisher Scientific, Yokohama, Japan). Qualities of RNA was determined by the Agilent 2100 Bioanalyzer (Agilent Technologies, Tokyo, Japan). RNA integrity number (RIN) values greater than 8 were used for subsequent analyses.
|
| Label |
Cy3
|
| Label protocol |
Total RNA (100 ng) was labeled with Cy3 using Low Input Quick Amp RNA Labeling kit, One-Color (Agilent Technologies) according to the manufacturer's instructions. Labelled cRNA were purified using an RNeasy mini kit (QIAGEN).. Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
600 ng of Cy3-labeled cRNA was fragmented and hybridized at 65 °C for 17 hours according to the manufacturer's instructions.
|
| Scan protocol |
Slides were scanned on the Agilent Microarray scanner (G2565CA).
|
| Data processing |
Data were extracted with Agilent Feature Extraction software version 11.0.1.1 (Agilent Technologies). Raw gene expression data were background corrected using the normexp method and normalized by the quantile method in Limma R package (Smyth et al.).
|
| |
|
| Submission date |
Nov 07, 2016 |
| Last update date |
Nov 06, 2018 |
| Contact name |
Ryo Kimura |
| E-mail(s) |
kimura.ryo.2w@kyoto-u.ac.jp
|
| Organization name |
Kyoto University Graduate School of Medicine
|
| Department |
Anatomy and Developmental Biology
|
| Street address |
Yoshida-Konoe-cho
|
| City |
Kyoto |
| ZIP/Postal code |
606-8501 |
| Country |
Japan |
| |
|
| Platform ID |
GPL16699 |
| Series (1) |
| GSE89594 |
Integrated network analysis reveals genotype-phenotype correlations in Williams syndrome |
|
