|
| Status |
Public on Oct 01, 2015 |
| Title |
PBMC-Control-8 |
| Sample type |
RNA |
| |
|
| Source name |
Peripheral blood
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Control
age: 44
Sex: Female
cell type: PBMC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
PBMCs were isolated in vaccutainer CPT Cell Preparation tubes with Sodium Citrate (BD biosciences, NJ, USA) from 16ml of blood. RNA was extracted by Trizol and enriched for the small RNA fraction (<40nt) using the Ambion Flash-PAGE system
|
| Label |
Cy5
|
| Label protocol |
miRNA were tailed with amine residues (mirVana™ miRNA Labelling Kit, Ambion) and labelled with Cy5 as recommended by the manufacturer
|
| |
|
| Hybridization protocol |
Standard Ambion mirVana bioarray hybridization protocol
|
| Scan protocol |
Array slides were scanned using a Genetic Microsystems GMS 418 scanner with a laser intensity of 95%, at multiple gain settings to avoid saturation of array spots. Intensity values were generated using Imagene V5.5 (BioDiscovery, USA) using automatic segmentation
|
| Description |
C267
Total RNA samples were size fractionated using the Ambion Flash-PAGE system to enrich for small RNA <40nt
|
| Data processing |
Un-background corrected median intensity values were corrected using Microarray valuation imp (MAVI) Pro 2.6.0 software (MWG biotech AG Ebersburg, Germany), which conducts a linear regression analysis on three gain scans of an array image to impute the values at the periphery of detection. Data was then normalized by averaging duplicate probe values and then filtering data to discard any data within 2 standard deviations of the mean of the empty control spots then median scaling, setting the median of each array to 100 and log transformed (base10), adapted from Shingara J et al 2005.
|
| |
|
| Submission date |
Jun 29, 2015 |
| Last update date |
Oct 01, 2015 |
| Contact name |
Robert Daniel Petty |
| E-mail(s) |
r.d.petty@qmul.ac.uk
|
| Organization name |
Barts Cancer Institute, Queen Mary, University of London
|
| Department |
Haemato-oncology
|
| Street address |
Charterhouse Square
|
| City |
London |
| ZIP/Postal code |
EC1M 6BQ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL3444 |
| Series (1) |
| GSE70371 |
The identification of miRNA biomarkers in CFS/ME peripheral blood samples |
|
