|
| Status |
Public on Mar 30, 2020 |
| Title |
methylation_30_Vehicle |
| Sample type |
genomic |
| |
|
| Source name |
primary cultured airway smooth muscle cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: primary cultured airway smooth muscle cell
donor: 30
treatment: Vehicle
asthma: No
age: 68
Sex: Male
imputedsmoking: No
race: EuropeanAmerican
|
| Treatment protocol |
ASMCs were exposed to IL-13 (10ng/mL), IL-17 (3ng/mL), IL-13+IL-17, or vehicle (10% FBS in PBS) for 24 hours prior to RNA and DNA extraction.
|
| Growth protocol |
ASMCs were cultured in 96-well Nusil coated plates in serum free media for 48 hours prior to cytokine exposure.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA from IL-13, IL-17, IL-13+IL-17, or vehicle-exposed airway smooth muscle cells was extracted and purified using the AllPrep Kit from QIAgen according to standard instructions
|
| Label |
Cy3,Cy5
|
| Label protocol |
Standard Illumina protocol.
|
| |
|
| Hybridization protocol |
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using standard Illumina scanner settings
|
| Description |
200517480038_R08C01
|
| Data processing |
Probes located on the sex chromosomes and those with detection P values > 0.01 in 75% of samples were removed. Probes mapping to more than one genomic location or overlapping with known SNPs (MAF>5% in either African Americans or European Americans) were also excluded. Data were processed using Minfi; Infinium type I and type II probe bias were corrected using SWAN. Raw probe values were corrected for color imbalance and background by control normalization.
normalized data file includes normalized (SWAN and background normalization) Average Beta
The raw data file "Unprocessed_Methylation_FinalGEO.csv" includes unmethylated and methylated signal intensities
|
| |
|
| Submission date |
Mar 04, 2020 |
| Last update date |
Mar 30, 2020 |
| Contact name |
Emma Thompson |
| E-mail(s) |
[email protected], [email protected]
|
| Organization name |
The University of Chicago
|
| Department |
Human Genetics
|
| Street address |
920 E 58th St, CLSC Rm 501
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL21145 |
| Series (2) |
| GSE146376 |
Genome-wide gene methylation study in primary cultured airway smooth muscle cells |
| GSE146377 |
Genome-wide gene expression and methylation studies in primary cultured airway smooth muscle cells |
|
