|
| Status |
Public on Oct 25, 2022 |
| Title |
250644 |
| Sample type |
RNA |
| |
|
| Source name |
Brushing of nasal epithelium
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: Female
age: 35
smoking status: Current smoker
fev1 % predicted: NA
cancer status: Cancer
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolated using miRNeasy kit from Qiagen, quantified using Nanodrop and quality determined using Bioanalyzer 2100 (Life Technologies). RNA was amplified using Ambion WT expression kit (Life Technologies).
|
| 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 GeneChip 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 nasal brushing of subject 250644.
|
| 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 1.54.0), using R version 3.5.1 and the Brainarray hugene10sthsentrezgcdf R package (version 22.0.0).
|
| |
|
| Submission date |
Aug 01, 2022 |
| Last update date |
Oct 25, 2022 |
| 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 |
GPL32540 |
| Series (2) |
| GSE210271 |
Smoking modulates different secretory subpopulations expressing SARS-CoV-2 entry genes in the nasal and bronchial airways (AEGIS nasal brushings) |
| GSE210661 |
Smoking modulates different secretory subpopulations expressing SARS-CoV-2 entry genes in the nasal and bronchial airways |
|
