|
| Status |
Public on Dec 05, 2009 |
| Title |
Rh3 - CD34+ -AMD3100 - miRNA - mAdbID:99561 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
EBV-infected B-cell Line Reference
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: EBV-infected B-cell line
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction with TRIZOL
Other: Cells were lysed with TRIzol reagent (Invitrogen, Carlsbad, CA) and total RNA was isolated according to the manufacturers instructions. RNA integrity was assessed by the presence of 28S and 18S bands using Agilent bioanalyzer and quantified using nanodrop with A260/A280 ratios > 2.0 after dilution in DEPC water.
|
| Label |
hy3
|
| Label protocol |
Hy3 Labeling Protocol
Other: Total RNA was labeled with Hy3 by using Exiqon miRNA labeling kit following the manufacturer's instructions.
|
| |
|
| Channel 2 |
| Source name |
CD34+ AMD3100 Mobilized - Hy5 label
|
| Organism |
Macaca mulatta |
| Characteristics |
tissue: blood
cell type: CD34+
|
| Treatment protocol |
Treatment type: compound
Agent: AMD3100
Treatment dose: 1 mg / kg (AMD3100)
Treatment time: 2 hours
In-vivo treatment: Rhesus macaques recieved one dose of AMD3100. Then the PBSC were collected by aphoresis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction with TRIZOL
Other: Cells were lysed with TRIzol reagent (Invitrogen, Carlsbad, CA) and total RNA was isolated according to the manufacturers instructions. RNA integrity was assessed by the presence of 28S and 18S bands using Agilent bioanalyzer and quantified using nanodrop with A260/A280 ratios > 2.0 after dilution in DEPC water.
|
| Label |
hy5
|
| Label protocol |
Hy5 Labeling Protocol
Other: Total RNA was labeled with Hy5 by using Exiqon miRNA labeling kit following the manufacturer's instructions.
|
| |
|
| |
| Hybridization protocol |
miRNA Sample Hybridization Protocol
Other: The miRNA were 3’-end tailed with amine-modified nucleotides and chemically coupled to HyDye fluors (Amersham Biosciences, Piscataway, NJ, USA).
|
| Scan protocol |
Creator: GenePix Pro 4.0.1.17
Scanner: GenePix 4000B [84945]
ScanPower: 33;; 33
LaserPower: 3.13;; 3.71
Temperature: 27.12
|
| Description |
mAdb experiment ID: 99561
|
| Data processing |
BRB ArrayTool Data Processing
Calculation Method: Raw data were retrieved in BRB-ArrayTools(http://linus.nci.nih.gov/BRBArrayTools.html) format for analysis and normalization. Following filter criteria was applied to the data set: 1. spots were excluded if intensity < 300, and spot size less than 25um 2. genes were filtered out if >80% of experiment with missing data values. 3. log2 transformed data were normalized using lowess smoother, and intensity ratios were truncated if greater than 64. Transcriptional data were process by averaging results in replicate experiments for the same genes.
|
| |
|
| Submission date |
Jul 02, 2009 |
| Last update date |
Dec 05, 2009 |
| Contact name |
Francesco Maria Marincola |
| E-mail(s) |
fmarincola@sidra.org
|
| Phone |
301-793-8210
|
| Organization name |
Sidra Medical and Research Center
|
| Street address |
Al Nasr Tower, AL Corniche Street, PO Box 26999
|
| City |
Doha |
| ZIP/Postal code |
PO Box 26999 |
| Country |
Qatar |
| |
|
| Platform ID |
GPL8794 |
| Series (1) |
| GSE16936 |
AMD3100 and G-CSF Mobilize Different CD34+ Cell Populations Based on Gene and miRNA Expression |
|
