|
| Status |
Public on Nov 15, 2015 |
| Title |
genomic DNA from aGBM primary culture 10 |
| Sample type |
genomic |
| |
|
| Source name |
aGBM primary culture 10
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: adult aGBM primary culture
|
| Growth protocol |
Cells were grown as monolayers in NS-A basal media (Stem Cell Technologies) supplemented with N2, B27, 75 μg/mL BSA (Sigma), 10 ng/mL rhEGF (Sigma), 10 ng/mL bFGF (Sigma) and 2 μg/mL heparin (Sigma).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA was extracted from cells using Qiagen DNeasy Kit according to standard instructions
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to the Illumina 450k Human Methylation Beadchip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Data processing |
Raw data (idat files) generated by Illumina GenomeStudio Software were imported into R program and Bioconductor package minfi was used to obtain methylated and unmethylated signals (non-normalized_data.txt) as well as beta and detection p-values (sample data table). We removed probes on the sex chromosomes and those with more than 90% sequence similarity to multiple genomic locations were excluded. The final dataset comprised of 392,879 autosomal probes.
|
| |
|
| Submission date |
Mar 24, 2015 |
| Last update date |
Nov 15, 2015 |
| Contact name |
Peter B Dirks |
| Organization name |
The Hospital for Sick Children
|
| Department |
Developmental and Stem Cell Biology
|
| Street address |
555 University Avenue
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 1X8 |
| Country |
Canada |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE63267 |
MLL5 orchestrates a cancer self-renewal state by repressing the histone variant H3.3 and globally reorganizing chromatin [methylation] |
|
