|
| Status |
Public on Apr 08, 2015 |
| Title |
Macrophage-oxLDL-2 |
| Sample type |
RNA |
| |
|
| Source name |
CD14+ derived macrophages - oxLDL
|
| Organism |
Homo sapiens |
| Characteristics |
background: Nepalese
cell type: Macrophage
agent: oxLDL
|
| Treatment protocol |
For foam cell formation (after 7 days) macrophages were treated with oxLDL (50mcg/ml, enodtoxin free, Copper oxidized). Control macrophages were treated with a matching buffer without oxLDL. Treatment duration - 48 hours.
|
| Growth protocol |
Purified CD14 positive peripheral blood monocytes were cultured for 7 days with 50ng/ml macrophage colony stimulating factor.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Primary human macrophages and foam cells were lyzed in the TRIZOL reagent and total RNA was extracted using the Invitrogen RNA PLUS extraction kit according to the manufacturers protocol (LifeTechnologies, Paisley UK). The integrity of the total RNA was analyzed on an Agilent Bioanalyzer 2100 (Agilent Technologies, Boeblingen, Germany).
|
| Label |
biotin
|
| Label protocol |
Total RNA was reverse tanscribed, amplified and biotinylated using the Illumina TotalPrep-96 RNA Amplification Kit(# 4393543 Ambion Inc., Austin, TX).
|
| |
|
| Hybridization protocol |
Biotinylated cRNA was hybridized to a single Illumina HumanHT-12 V4 BeadCHIP at 58 degrees C for 18 hours.
|
| Scan protocol |
The BeadCHIP was scnned using the Illumina Iscanner and data pre-processed using the Illumina Bead Studio to correct for local background effects, remove outlier beads, compute average bead signal and SD for each probe and gene and calculation of detection P-values using negative controls present on the array.
|
| Description |
E1
|
| Data processing |
The matrix of non-normalized values includes Bead Studio Output and detection P values output from the 'scan protocol'. Data were then processed using the LUMI pipeline in R. Data were subjected to VST transformation and robust spline normalization.
|
| |
|
| Submission date |
Feb 04, 2014 |
| Last update date |
Apr 08, 2015 |
| Contact name |
Christopher O'Callaghan |
| E-mail(s) |
chris.ocallaghan@ndm.ox.ac.uk
|
| Phone |
+44 (0)1865 287794
|
| Organization name |
University of Oxford
|
| Department |
Nuffield Department of Medicine
|
| Lab |
O'Callaghan Lab - Henry Wellcome Building for Molecular Physiology
|
| Street address |
Roosevelt Drive
|
| City |
Oxford |
| State/province |
Oxfordshire |
| ZIP/Postal code |
OX3 7BN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL10558 |
| Series (2) |
| GSE54666 |
Gene expression in primary human macrophages and foam cells |
| GSE54975 |
Lipid-induced epigenomic changes in human macrophages identify a coronary artery disease associated variant that regulates PPAP2B expression through altered C/EBP-beta binding |
|
