|
| Status |
Public on Apr 10, 2017 |
| Title |
PC252N |
| Sample type |
genomic |
| |
|
| Source name |
prostate benign tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: prostate benign tissue
age: 65
ethinicity: Caucasian
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from tissue lysate using the Qiagen AllPrep DNA/RNA mini kit
|
| Label |
Cy5 and cy3
|
| Label protocol |
Labeling was performed using standard manufacture protocol.
|
| |
|
| Hybridization protocol |
hyb was performed using standard manufacture protocol
|
| Scan protocol |
scan was performed using standard manufacture protocol
|
| Data processing |
Unmethylated and methylated signal intensities in matrix_signal_intensities.txt Series supplementary file.
We converted data points that were not significant above background intensity to NA. We removed CpGs having greater than 10% missing values prior to normalization. Data was normalized using the Combat R package. Post-ComBat normalization, we observed that Infinium I and Infinium II assays showed two distinct bimodal b-value distributions, so we developed a regression method to convert the type I and type II assays to a single bimondal b-distribution corresponding to Reduced Representation Bisulfite Sequencing b-values. After this conversion, any beta score greater than 1 was assigned a 1, and any beta score less than 0 was assigned a 0. The equations for correction are: Infinium I : RRBS = 0.00209 + 0.4377 x Methyl450 + 0.6303 x Methyl4502 ; Infinium II : RRBS = -0.01146 + 0.2541 x Methyl450 + 0.9832 x Methyl4502
|
| |
|
| Submission date |
Jan 18, 2016 |
| Last update date |
Apr 10, 2017 |
| Contact name |
Marie K Kirby |
| Organization name |
HudsonAlpha Institute for Biotechnology
|
| Street address |
601 Genome Way NE
|
| City |
Huntsville |
| State/province |
AL |
| ZIP/Postal code |
35806 |
| Country |
USA |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE76938 |
Illumina M450 profiling of human prostate cancer tissue and benign prostate tissue |
|
