|
| Status |
Public on Nov 01, 2017 |
| Title |
oxPAPC control-treated HUVECs replicate 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Human Umbilical Vein Endothelial Cells (HUVECs)
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: oxPAPC control medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted with Trizol following manufacturer's instructions
|
| Label |
Hy3
|
| Label protocol |
200 ng total RNA from sample and reference was labelled with Hy3 and Hy5 fluorescent label, respectively, using miRCURY LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer.
|
| |
|
| Channel 2 |
| Source name |
Total RNA common reference pool
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: reference
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted with Trizol following manufacturer's instructions
|
| Label |
Hy5
|
| Label protocol |
200 ng total RNA from sample and reference was labelled with Hy3 and Hy5 fluorescent label, respectively, using miRCURY LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer.
|
| |
|
| |
| Hybridization protocol |
The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA array version 11.0 (Exiqon, Denmark )according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria).
|
| Scan protocol |
The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA)
|
| Description |
oxPAPC_ctrl2
Biological replicate 2 of 3 treated with oxPAPC control medium for 4h prior collection
|
| Data processing |
The image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA). The quantified signals were background corrected (Normexp with offset value 10 – Ritchie et al., 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.
All capture probes with both Hy3 and Hy5 signals lower than 1.5x of the median signal intensity of the given slide, or for which calling failed, are excluded.
|
| |
|
| Submission date |
Aug 10, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Suvi Kuosmanen |
| Organization name |
University of Eastern Finland
|
| Street address |
Neulaniementie 2
|
| City |
Kuopio |
| ZIP/Postal code |
70211 |
| Country |
Finland |
| |
|
| Platform ID |
GPL15829 |
| Series (1) |
| GSE102501 |
Human umbilical vein endothelial cells (HUVECs): VEGF vs. ctrl, oxPAPC vs. ctrl |
|
