|
| Status |
Public on Dec 31, 2017 |
| Title |
DAC-treated retroviral 4F MSC iPSC p25 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
DAC-treated MMW2 iPS p25
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: MMW2 iPS p25
passage: p25
sample type: retroviral mesenchymal stem cell iPSC (Ohm et al. 2011 Cancer Res 70:7662-7673 2010)
treatment: 5 micromolar 5-AZA (DAC) for 96 hours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction based on the manufacturer's instructions, followed by RNeasy cleanup as per the manufacturer's instructions.
|
| Label |
Cy5
|
| Label protocol |
Agilent low RNA input linear amplification kit.
|
| |
|
| Channel 2 |
| Source name |
Control-treated MMW2 iPS p25
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: MMW2 iPS p25
passage: p25
sample type: retroviral mesenchymal stem cell iPSC (Ohm et al. 2011 Cancer Res 70:7662-7673 2010)
treatment: 1x PBS for 96 hours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction based on the manufacturer's instructions, followed by RNeasy cleanup as per the manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
Agilent low RNA input linear amplification kit.
|
| |
|
| |
| Hybridization protocol |
Agilent Gene Expression Hybridization Kit using the manufacturer's protocol.
|
| Scan protocol |
Microarrays are scanned with the Agilent G2565BA microarray scanner under default settings recommended by Agilent Technologies for expression microarrays with 100% PMT and 10 micrometer resolutions. Data are extracted using Feature Extraction Software v8.1 (Agilent Technologies) under default settings for expression microarrays.
|
| Description |
Individual sample
|
| Data processing |
Loess normalization as implemented in the Limma package from Bioconductor.
|
| |
|
| Submission date |
Mar 07, 2013 |
| Last update date |
Dec 31, 2017 |
| Contact name |
Elias Thomas Zambidis |
| Organization name |
Johns Hopkins School of Medicine
|
| Department |
Oncology
|
| Street address |
733 N. Broadway
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL4133 |
| Series (2) |
| GSE44941 |
Cancer-related epigenome changes among induced pluripotent stem cell lines |
| GSE82233 |
Quality of reprogramming to induced pluripotency as a function of reprogramming method |
|
