|
| Status |
Public on Jun 17, 2011 |
| Title |
Plasma_CS_rep5 |
| Sample type |
RNA |
| |
|
| Source name |
Cloudy Supernatant
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: plasma-derived
subfraction: cloudy supernatant
disease state: healthy
population: Caucasian
|
| Treatment protocol |
All samples were initially spun at 1700g for 10 minutes to separate the plasma from the Buffy Coat and Red Blood Cells. Leukocytes were separately isolated from whole blood fractionated through Ficoll-Hypaque gradients. The plasma was re-centrifuged at 2000g for 10 minutes to obtain the Supernatant 1 (S1) and Pellet 1 (P1) fractions. The S1 fraction was additionally centrifuged at 12000g for 10 minutes to generate the Supernatant 2 (S2) and Pellet 2 (P2) fractions.
|
| Growth protocol |
Blood was drawn in sodium EDTA tubes and processed within 4 hours of draw.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol-LS, Phenol:Chloroform and purified through Ambion mirVANA columns.
|
| Label |
biotin
|
| Label protocol |
A total of 500-1000ng of total RNA was labelled using the Genisphere HSR labelling Kit (http://www.genisphere.com/array_detection_flashtag_biotin.html).
|
| |
|
| Hybridization protocol |
The total amount of RNA was hybridized to the arrays for 16 hours at 48C with rotation at 60rpm.
|
| Scan protocol |
Samples were scanned using the GCS 3000 7G Scanner and processed using miRNA_1-0_2xgain library files.
|
| Description |
CS_5
miRNA expression data.
|
| Data processing |
The data was preprocessed using the Affymetrix miRNA QC tool where Individual feature intensities were flagged by detection calls, background subtracted, transformed through addition of a small constant (value equal to 16) and median summarized. Non-normalized data was analyzed to preserve the individual distributions for rank correlation analysis.
|
| |
|
| Submission date |
Feb 10, 2011 |
| Last update date |
Jun 17, 2011 |
| Contact name |
Radha Duttagupta |
| E-mail(s) |
Radharani_Duttagupta@affymetrix.com
|
| Phone |
408-731-5691
|
| Fax |
408-731-5463
|
| Organization name |
Affymetrix
|
| Department |
Applied Research
|
| Street address |
3450 Central Expressway
|
| City |
Santa Clara |
| State/province |
CA |
| ZIP/Postal code |
95051 |
| Country |
USA |
| |
|
| Platform ID |
GPL8786 |
| Series (2) |
| GSE27230 |
Analysis of the impact of cellular miRNA signatures on the profiles of circulating miRNA biomarkers (fractionation data) |
| GSE27256 |
Impact of cellular miRNAs on the biomarker signatures of circulating miRNAs |
|
