|
| Status |
Public on Feb 13, 2018 |
| Title |
NA19239_methylation |
| Sample type |
genomic |
| |
|
| Source name |
iPSC
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: iPSC
gender: Male
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from samples using Zymo dual extraction kits (Zymo Research)
|
| Label |
Cy3/Cy38
|
| Label protocol |
Standard illumina protocols
|
| |
|
| Hybridization protocol |
The samples were bisulphite-converted and hybridized to the Infinium HumanMethylation450 BeadChip at the University of Chicago Functional Genomics facility.
|
| Scan protocol |
scan protocol not provided
|
| Description |
iPSC
Bisulfite Converted DNA
|
| Data processing |
To ensure high data quality, probes were mapped to a bisulfite converted genome and only uniquely mapped probes were retained. Additionally, probes with low detection (P > 0.01) in more than 25% of samples were discarded. Samples were than normalized using the SWAN method to control for different probe types. Finally, red and green color channels were independently quantile normalized.
We transformed methylation levels to a standard normal within each individual and five principal components were removed to account for unknown variation
|
| |
|
| Submission date |
Feb 13, 2018 |
| Last update date |
Feb 13, 2018 |
| Contact name |
Nicholas E Banovich |
| Organization name |
University of Chicago
|
| Department |
Human Genetics
|
| Lab |
Gilad
|
| Street address |
920 E. 58th Street, CLSC 317
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60453 |
| Country |
USA |
| |
|
| Platform ID |
GPL21145 |
| Series (2) |
| GSE89895 |
Impact of regulatory variation across human iPSCs and differentiated cells |
| GSE110544 |
Impact of regulatory variation across human iPSCs and differentiated cells [methylation] |
|
