|
| Status |
Public on Nov 30, 2015 |
| Title |
Sample1_NPC_4FP53 |
| Sample type |
genomic |
| |
|
| Source name |
iPSC-derived human Neural Progenitor Cell, P53 knockdown and inhibition of the PI3K and MAPK signaling pathways
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Neural Progenitor Cell
treatment: Inhibition of P53 and PI3K and MAPK signaling pathways
cell line: iPSC derived
|
| Growth protocol |
Neurobasal media (Invitrogen) supplemented with N2 (Invitrogen), B27 (Invitrogen), and FGF2 (10 ng/ml; preprotech)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated using the DNeasy kit (69504, Qiagen), quantified (Qubit dsDNA BR Assay Kits, Life Technologies, Inc.) and bisulfite converted (EZDNA Methylation Kit, Zymo Research) according to the manufacturer’s protocol.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
Standard Illumina Protocol
|
| Scan protocol |
Arrays were imaged using Illumina's HiScan System using standard recommended Illumina scanner setting
|
| Data processing |
Samples were normalized and filtered using the statistical programming language R (http://www.r-project.org/) (v.3.0.1) and the R package minfi (v.1.6.0). Briefly, samples were first control-normalized using Illumina’s internal bead controls and probes with a detection P value > 0.01 in at least one sample were discarded. The samples were then SWAN normalized using the minfi package and β values (Methylated allele intensity/ Unmethylated allele intensity + Methylated allele intensity) were exported. Probes with less than a max β – min β of 0.5 were removed
|
| |
|
| Submission date |
Mar 25, 2015 |
| Last update date |
Nov 30, 2015 |
| Contact name |
Robert E Morey |
| E-mail(s) |
robmoreyucsd@gmail.com, remorey@health.ucsd.edu
|
| Organization name |
UCSD
|
| Department |
Pathology
|
| Lab |
Parast
|
| Street address |
2880 Torrey Pines Scenic Dr
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE67283 |
Establishment of tractable human iPSC-based models for the study and targeting of glioma initiation (Methlyation) |
| GSE67286 |
Establishment of human iPSC-based models for the study and targeting of glioma initiating cells |
|
