|
| Status |
Public on Feb 01, 2013 |
| Title |
No treated control #3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
human lung fibroblasts MRC-5 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: lung fibroblasts MRC-5
agent: untreated
time: control
|
| Treatment protocol |
After overnight serum starvation, cells were treat with TGF beta1 for 48 h or 96 h
|
| Growth protocol |
MEM containing 10% FBS, 37 degree and 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Qiagen RNAeasy kit following manufacturer's instructions
|
| Label |
Hy3
|
| Label protocol |
1000 ng total RNA from sample and reference was labelled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer
|
| |
|
| Channel 2 |
| Source name |
common reference (pooled total RNA from human lung fibroblasts MRC-5 cells that were untreated, treated with TGF beta1 for 48 and 96h)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: lung fibroblasts MRC-5
sample type: common reference (pooled total RNA of equal amount of the 9 samples)
|
| Treatment protocol |
After overnight serum starvation, cells were treat with TGF beta1 for 48 h or 96 h
|
| Growth protocol |
MEM containing 10% FBS, 37 degree and 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Qiagen RNAeasy kit following manufacturer's instructions
|
| Label |
Hy5
|
| Label protocol |
1000 ng total RNA from sample and reference was labelled with Hy3™ and Hy5™ fluorescent label, respectively, using the 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 5th Generation (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBASE version 15.0 at the Sanger Institute. The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria)
|
| Scan protocol |
After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA).
|
| Description |
Biological replicate 3 of 3. MRC-5 cells, untreated.
'1_Exiqon*.txt' and '0_Exiqon*.txt' represent the raw data for Hy3 and Hy5, respectively.
|
| Data processing |
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.
|
| |
|
| Submission date |
Feb 01, 2013 |
| Last update date |
Feb 01, 2013 |
| Contact name |
Gang Liu |
| Organization name |
University of Alabama at Birmingham
|
| Department |
Medicine
|
| Street address |
901 19TH ST S
|
| City |
Birmingham |
| State/province |
Alabama |
| ZIP/Postal code |
35294 |
| Country |
USA |
| |
|
| Platform ID |
GPL11432 |
| Series (1) |
| GSE43992 |
miRNA in human lung fibroblasts |
|
