|
| Status |
Public on Jun 26, 2018 |
| Title |
Subject 11009 baseline |
| Sample type |
RNA |
| |
|
| Source name |
Bronchial epithelial cells
|
| Organism |
Homo sapiens |
| Characteristics |
smoke exposure: baseline
rin: 6.6
Sex: female
|
| Treatment protocol |
Study participants were asked to refrain from cigarette smoking for at least two days (verified by exhaled CO < 6 ppm) and then smoke three cigarettes in the span of one hour. Subjects then underwent fiberoptic bronchoscopy after 24 hours where samples were collected. In like manner, subjects abstained from smoking and underwent bronchoscopy at a separate time at least 6 weeks from the post-smoking bronchoscopy to serve as an unexposed baseline sample (also verified by exhaled CO < 6 ppm). In both instances, bronchial brushings were collected from the 1st and 2nd subsegmental branches of the left lower lobe.
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The brushes were immediately placed in TRIzol reagent (Invitrogen) after removal from the bronchoscope and kept at -80°C until RNA isolation was performed. Total RNA was isolated using the miRNeasy Mini Kit (Qiagen, Valencia, CA). Integrity of the RNA samples was assessed by Agilent BioAnalyzer, and purity of the RNA was confirmed using a NanoDrop spectrophotometer.
|
| Label |
biotin
|
| Label protocol |
Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
The labeled, fragmented DNA was hybridized to the Affymetrix Human Gene 1.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.
|
| Scan protocol |
After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.
|
| Description |
Gene expression data from bronchial epithelial cells collected by bronchoscopic brushing at baseline.
|
| Data processing |
Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray hugene10sthsentrezg R package (version 16.0.0).
|
| |
|
| Submission date |
Mar 24, 2017 |
| Last update date |
Jun 27, 2018 |
| Contact name |
Adam C Gower |
| E-mail(s) |
agower@bu.edu
|
| Phone |
617-358-7138
|
| Organization name |
Boston University School of Medicine
|
| Department |
Department of Medicine
|
| Lab |
Division of Computational Biomedicine
|
| Street address |
72 East Concord Street, E632
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
| |
|
| Platform ID |
GPL17244 |
| Series (1) |
| GSE97010 |
The Impact of Acute Exposure to Cigarette Smoke on Airway Gene Expression |
|
