|
| Status |
Public on Feb 23, 2018 |
| Title |
850K_GBM80 |
| Sample type |
genomic |
| |
|
| Source name |
tumor tissue from Patient Derived Xenograph
|
| Organism |
Homo sapiens |
| Characteristics |
age: tumor tissue from Patient Derived Xenograph
gender: genomic DNA
|
| Growth protocol |
Tumor tissue from Patient-Derived Xenograft (PDX) were mechanically dissociated and selected in stem cell culture medium (ThermoFisher, StemPro NSC SFM A1050901) containing L-glutamin and Penicillin-Streptomycin in laminin (#L2020) -coated flasks to reduce culture condition-introduced heterogeneity. Neural stem cells were expanded on Matrigel (CORNING 356230) or fibronectin-coated 6-well plate in stem cell growth medium (GM) containing DEME/F12 plus Glutamax (Life Technologies 10565-018), BIT9500 Serum Substitute (1x, Stem Cell Technologies 09500), Heparin (20ug/mL Sigma H3149), Primocin (1x, InvivoGen ant-pm-1), human bFGF (20ng/Ml, Stemgent 03-0002), human EGF (20ng/mL, R&D Biosystems 236-EG).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated and purified from homogenized liver tissue using a serial phenol: chloroform extraction. Trizol reagent was used for extracting total RNA following the manufacturer’s protocol.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Description |
genomic DNA from PDX tumor
tumor tissue from Patient Derived Xenograph
|
| Data processing |
Subset-quantile Within Array Normalization (SWAN) via R Bioconductor package minfi
|
| |
|
| Submission date |
Dec 15, 2016 |
| Last update date |
Feb 23, 2018 |
| Contact name |
Keith Robertson |
| Organization name |
Mayo Clinic
|
| Department |
Molecular Pharmacology and Experimental Therapeutics
|
| Street address |
200 1st St SW
|
| City |
Rochester |
| State/province |
MN |
| ZIP/Postal code |
55905 |
| Country |
USA |
| |
|
| Platform ID |
GPL21145 |
| Series (2) |
| GSE92462 |
Characterizing the epigenome of glioma stem cells (Methylation BeadChip) |
| GSE92469 |
Characterizing the epigenome of glioma stem cells |
|
