|
| Status |
Public on Oct 01, 2018 |
| Title |
WT_mk21_methylation |
| Sample type |
genomic |
| |
|
| Source name |
WT PanNET for ATRX / DAXX and MEN1
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Pancreatic neuroendocrine tumors (PanNETs)
genotype: WT for ATRX/DAXX/MEN1
pannet subtype: A-D-M WT PanNETs
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted and purified from PanNET samples using Qiagen DNeasy Kit according to standard instructions
|
| Label |
Cy3, Cy5
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Description |
DNA CpG Methylation profile for Human PanNETs
|
| Data processing |
All IDAT files were processed in R using ChAMP package with QC, normalization (FunctionNormalization) and Differentially methylated probes
Normalized data using FunctionNormalization method within ChAMP package and obtained Beta values for all quality passed probe
|
| |
|
| Submission date |
Jul 30, 2018 |
| Last update date |
Oct 01, 2018 |
| Contact name |
SAURABH V LADDHA |
| E-mail(s) |
[email protected]
|
| Organization name |
Rutgers Cancer Institute of New Jersey
|
| Department |
Center for Systems and Computational Biology
|
| Street address |
195 Little Albany Street
|
| City |
New Brunswick |
| State/province |
NEW JERSEY |
| ZIP/Postal code |
08901-1914 |
| Country |
USA |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE117852 |
Methylation Heterogeneity within Human non-functional Pancreatic neuroendocrine tumors (PanNETs) |
| GSE117853 |
Gene expression and methylation profile of Human non-functional Pancreatic neuroendocrine tumors (PanNETs) |
|
