|
| Status |
Public on Jul 05, 2024 |
| Title |
Sample10 |
| Sample type |
genomic |
| |
|
| Source name |
Nasal-epithelial Tissue
|
| Organism |
Homo sapiens |
| Characteristics |
vape_6mo_lab: Did Not Vape in Last 6 Months
age: 17
Sex: Female
recruitment_center: Aurora
ruv1: 0.137696786249186
ruv2: -0.341047400260943
|
| Treatment protocol |
To measure methylation at approximately 850,000 single CpG sites across the genome, we used Illumina’s Infinium Human Methylation 850k BeadChip on bisulfite-treated samples. 0.85-1.00 µg DNA were bisulfite converted using the Zymo EZ DNA Methylation kit (Zymo Research, Orange, CA). Each conversion assay included a commercially available positive and negative control sample.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Bisulfite converted samples formed the input for the Illumina Infinium Methylation assay using the Human Methylation 850k BeadChips (Illumina Inc, San Diego, CA).
|
| Label |
Cy3, Cy5
|
| Label protocol |
The labeling, hybridization, and scanning procedures were performed on the Illumina IScan system in the University of Colorado Genomics Core.
|
| |
|
| Hybridization protocol |
The labeling, hybridization, and scanning procedures were performed on the Illumina IScan system in the University of Colorado Genomics Core.
|
| Scan protocol |
The labeling, hybridization, and scanning procedures were performed on the Illumina IScan system in the University of Colorado Genomics Core. This analysis was performed in 11 adolescents who self-identified as vaping in the last 6 months and 36 who had not. All samples were assayed once (no technical replicates) with 6 arrays (8 samples per array) performed in 1 batch.
|
| Description |
Nasal-epithelial Tissue Swab
|
| Data processing |
Samples were evaluated for a low mean-intensity to identify potential outliers with low-quality methylation values.
probes were removed due to non-unique mapping, influence by SNPs, or by having a detection p-value > 0.05 in at least 10% of samples.
Background subtraction using normal-exponential deconvolution using out-of-band probes (noob) to make Type I and Type II probes comparable
BMIQ normalization was considered a priori due to a concern for lack of within-array normalization as interpreted from diagnostic plots.
A non-linear dye bias correction was used to make the red and green signal intensities (Type-I) more comparable
|
| |
|
| Submission date |
Aug 04, 2023 |
| Last update date |
Jul 05, 2024 |
| Contact name |
Sunita Sharma |
| E-mail(s) |
sunita.sharma@cuanschutz.edu
|
| Organization name |
University of Colorado - Anschutz Medical Campus
|
| Department |
Anschutz Campus - Sch of Med - Pulmonary Sciences
|
| Street address |
13001 East 17th Place
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL21145 |
| Series (2) |
| GSE240130 |
The impact of vaping on adolescent lung function and nasal epithelial gene expression [Genome wide DNA methylation] |
| GSE240132 |
The impact of vaping on adolescent lung function and nasal epithelial gene expression |
|
