|
| Status |
Public on Aug 10, 2015 |
| Title |
HCAEC_si_RNF2 |
| Sample type |
RNA |
| |
|
| Source name |
Human coronary artery endothelial cell, siRNF213, replicate2
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: coronary artery endothelial cell
condition: siRNF213
|
| Treatment protocol |
Transfection of siRNA was conducted using Lipofectamine RNAiMAX (Invitrogen) according to the manufacturer’s protocol.
|
| Growth protocol |
HCAECs were cultured in EGM-2MV (Lonza) containing 10% fetal calf serum. All cell cultures were maintained at 37˚C in normoxic environments with 5% CO2 and 100% humidity.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)
|
| Label |
Cy3
|
| Label protocol |
cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).
|
| |
|
| Hybridization protocol |
cRNA was hybridized to a 44K 60-mer oligomicroarray SurePrint G3 Human GE Microarray Kit 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.
|
| Scan protocol |
The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).
|
| Description |
Gene expression upon treatment with siRNF213
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of four samples were normalized by the quantile algorithm with the Bioconductor.
|
| |
|
| Submission date |
Oct 15, 2014 |
| Last update date |
Aug 10, 2015 |
| Contact name |
Kazuhiro Ohkubo |
| E-mail(s) |
kohkubo@pediatr.med.kyushu-u.ac.jp
|
| Organization name |
Graduate School of Medical Sciences, Kyushu University
|
| Department |
Department of Pediatrics
|
| Street address |
3-1-1, Maidashi, Higashi-ku
|
| City |
Fukuoka |
| State/province |
Fukuoka |
| ZIP/Postal code |
812-8582 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17077 |
| Series (1) |
| GSE62348 |
Gene expression profile in HCAECs transfected with RNF213 siRNA |
|
