|
| Status |
Public on Jan 31, 2010 |
| Title |
Lung_self-limiting_biological_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Lung biopsy sample from patient with nodular, self-limiting disease
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Lung biopsy
disease type: Nodular, self-limiting (N-SL)
cohort: First
date array hybridised: 20/03/08
gender: Female
age: 36
|
| Treatment protocol |
Samples were obtained by standard bronchial biopsy protocols (CT-targeted transbronchial biopsy) at the point of clinical presentation. Patients were followed up for 2 years and classified into 'nodular, self-limiting' and 'progressive, fibrotic' pulmonary disease groups, based on symptons, pulmonary function tests and CT scans
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from lung biopsies was extracted within 24 hours using the Qiagen RNeasy Mini kit, as per manufacturer's instructions
|
| Label |
Biotin
|
| Label protocol |
Isolated total RNA was used with GeneChip WT cDNA synthesis and amplification kit (Affymetrix#900672) to produce fragmented single-stranded DNA, which was labeled using terminal labeling kit (Affymetrix#900670) to generate biotin-labeled sense targeted DNA probes.
|
| |
|
| Hybridization protocol |
Fragmented and labeled DNA (2500ng) was used in 100 µl hybridization cocktail containing control oligonucleotide B2 (50pM) and hybridization controls (Affymetrix #900454), of which 80 µl was hybridised to each chip for 17h in the hybridization oven at 45ºC and rotating at 60rpm. Arrays were processed using Genechip Fluidics Station 450 according to recommended protocols (FS450_007) of double-staining and post-hybridization washes using GeneChip hybridization, wash and stain kit (Affymetrix #900720).
|
| Scan protocol |
Fluorescent images were captured using gene Array scanner 3000 and GCOS 1.2 software (Affymetrix).
|
| Description |
Lung_self-limiting_biological_rep2
|
| Data processing |
Raw data were processed using Affymetrix Power Tools to generate RMA normalised intensities and subsequent analysis was carried out using R and BioConductor packages. Differential expression was assessed using the limma package and included an effect for cohort.
|
| |
|
| Submission date |
Jan 20, 2010 |
| Last update date |
Jan 20, 2010 |
| Contact name |
Ling-Pei Ho |
| E-mail(s) |
ling-pei.ho@imm.ox.ac.uk
|
| Organization name |
Weatherall Institute for Molecular Meicine, University of Oxford
|
| Department |
MRC Human Immunology Unit
|
| Street address |
John Radcliffe Hospital
|
| City |
Oxford |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE19976 |
Gene expression analysis of lung biopsies from patients with two different forms of pulmonary sarcoidosis |
|
