|
| Status |
Public on Aug 20, 2008 |
| Title |
Periodontitis Neutrophils rep1 |
| Sample type |
RNA |
| |
|
| Source name |
chronic Periodontitis patient neutrophils
|
| Organism |
Homo sapiens |
| Characteristics |
RNA from 4 chronic periodontitis patients pooled
|
| Biomaterial provider |
University of Birmingham
|
| Treatment protocol |
Venous blood collected from the ante-cubital fossa into Vacutainer tubes containing lithium heparin (17 IU/ml). Neutrophils were isolated from venous blood (lithium heparin) using a discontinuous Percoll gradient (d=1.079:1.098) followed by erythrocyte lysis (0.83% NH4Cl containing 1% KHCO3, 0.04% Na2EDTA.2H2O & 0.25% bovine serum albumen). Isolated cells were re-suspended in PBS supplemented with glucose (1mM) and cations (1mM MgCl2, 1.5mM CaCl2) at 1x106 cells/ml. Cell viability, typically >98%, was determined using dye exclusion (trypan blue).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
phenol/chloroform extraction (Sigma, Trizol), the aqueous phase was combined with 70% ethanol and added to an RNeasy mini-column (Qiagen). Subsequent purification and DNase treatment were performed as recommended by the manufacturer (Qiagen). RNA was eluted in sterile water
|
| Label |
Biotin
|
| Label protocol |
DNase digested total RNA was used to generate double-stranded cDNA using Super-Script reagents (Life Technologies) and a T7-linked oligo(dT) primer. cRNAs were synthesized using the EnzoBioarray High Yield RNA transcript labeling kit (Affymetrix) and resulting biotinylated labeled cRNA was subsequently fragmented into 35- to 200-bp lengths using Fragmentation buffer (Affymetrix).
|
| |
|
| Hybridization protocol |
As per manufactures instructions
|
| Scan protocol |
As per manufactures instructions
|
| Description |
N/A
|
| Data processing |
MAS 5
|
| |
|
| Submission date |
Aug 19, 2008 |
| Last update date |
Sep 01, 2016 |
| Contact name |
Helen Joan Wright |
| Organization name |
University of Birmingham
|
| Department |
Oral Biology
|
| Street address |
St Chads Queensway
|
| City |
Birmingham |
| State/province |
West Midlands |
| ZIP/Postal code |
B4 6NN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL96 |
| Series (1) |
| GSE12484 |
Periodontitis is associated with a type-1 interferon signature in peripheral blood neutrophils |
|
| Relations |
| Reanalyzed by |
GSE86363 |
