|
| Status |
Public on Aug 02, 2013 |
| Title |
NATURI_54_Nasal mucosa_AsmNoEx_day 2 |
| Sample type |
RNA |
| |
|
| Source name |
Nasal mucosa from asthmatic without exacerbation at day 2 of cold symptoms
|
| Organism |
Homo sapiens |
| Characteristics |
group: Asthmatic_no exacerbation
gender: female
age: 41 yrs
time point (visit): Day 2 (V1)
tissue: Nasal mucosa
|
| Treatment protocol |
Nasal mucosa was sampled using Rhinoprobe and stored in RLT lysis buffer (QIAGEN) at -80C
|
| Growth protocol |
In vivo sampling of nasal mucosa of the course of naturally occuring colds.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from nasal mucosa samples using RNeasy Mini Kit (QIAGEN) with the addition of a DNAse treatment (1U/mL fro 1hr at 37C; Promega) and re-purification phase. Extracted RNA was further purified using the RNA Clean and Concentrator (ZYMO Research) and quality assesed by Agilent 2100 Bioanalyzer (Agilent Technologies).
|
| Label |
Cy3
|
| Label protocol |
RNA was amplified and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol (Agilent)
|
| |
|
| Hybridization protocol |
Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays (Agilent). Hybridizations were performed for 14 hrs, according to the manufacturers protocol (Agilent).
|
| Scan protocol |
Arrays were scanned using the Agilent microarray scanner (Agilent) and raw signal intensities were extracted with Feature Extraction v10.1 software (Agilent).
|
| Description |
NATURI_54
Gene expression in the nasal mucosa of an individual with asthma, who did not experience an episode of exacerbation, two days after the onset of cold symptoms
|
| Data processing |
Processed data are presented in one data matrix with the 36,866 Agilent Probe IDs (out of possible 41108 and 36926, respectively), which are represented in both platform records. This dataset was normalized using the quantile normalization method that is proposed by Bolstad et al Bioinformatics. 2003 Jan 22;19(2):185-93. No background subtraction was performed, and the median feature pixel intensity was used as the raw signal before normalization.
|
| |
|
| Submission date |
Apr 18, 2013 |
| Last update date |
Aug 02, 2013 |
| Contact name |
Peter McErlean |
| Organization name |
Northwestern University
|
| Department |
Allergy Immunology
|
| Lab |
Avila
|
| Street address |
240 E. Huron, McGaw M-530h
|
| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60613 |
| Country |
USA |
| |
|
| Platform ID |
GPL16981 |
| Series (1) |
| GSE46171 |
Asthmatics with exacerbation during acute respiratory illness exhibit unique transcriptional signatures. |
|
