|
| Status |
Public on Nov 30, 2015 |
| Title |
SAMPLE 5_NPC P53_1_4F |
| Sample type |
RNA |
| |
|
| 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 |
total RNA |
| Extraction protocol |
RNA was purified using the RNeasy Plus mini kit (74134, Qiagen). Purity and integrity of the RNA samples were assessed by spectrophotometry and nanoelectrophoresis using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the Nano lab-on-a-chip assay for total eukaryotic RNA using Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).
|
| Label |
biotin
|
| Label protocol |
200 ng of total RNA were amplified using the Ambion® WT Expression Kit (Ambion/Applied Biosystems) and labeled using the WT Terminal Labeling Kit (Affymetrix).
|
| |
|
| Hybridization protocol |
The labeled material was then hybridized to Human Gene 1.0 ST Array (Affymetrix) for 16 hours at 45ºC and 60 rpm in a GeneChip® Hybridization Oven 640.
|
| Scan protocol |
The stained array was scanned using an Affymetrix GeneChip® Scanner 3000 7G.
|
| Data processing |
Samples were normalized and log transformed and then filtered using a variance filter (σ/σ max) of 0.2. Sample7 was considered an outlier sample and was removed from further analysis.
Microarray analysis is done in R (version 2.15) with Bioconductor packages i.e. affy and limma. After quality control of raw data, it was background corrected, quantile-normalized and log2 transformed.
|
| |
|
| Submission date |
Mar 25, 2015 |
| Last update date |
Dec 01, 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 |
GPL6244 |
| Series (2) |
| GSE67284 |
Establishment of tractable human iPSC-based models for the study and targeting of glioma initiation (Expression) |
| GSE67286 |
Establishment of human iPSC-based models for the study and targeting of glioma initiating cells |
|
