|
| Status |
Public on Jan 31, 2018 |
| Title |
VP16-SOX9∆TAD-2 |
| Sample type |
RNA |
| |
|
| Source name |
VP16-SOX9∆TAD-ires-GFP transfected EndoC-ßH1 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: EndoC-ßH1
treatment: VP16-SOX9∆TAD-ires-GFP transfected
|
| Treatment protocol |
EndoC-ßH1 cells were transfected and sorted 48h post-transfection prior to RNA extraction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy Micro kit (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Total RNA is reverse transcribed following the GeneChip™ WT PLUS Reagent Kit (applied biosystems). Briefly, the resulting double strand cDNA is used for amplification based on SPIA technology. After purification according to Nugen protocol, 3.6 ug of Sens Target DNA are fragmented and biotin labelled using Encore Biotin Module kit (Nugen).
|
| |
|
| Hybridization protocol |
After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® Human Gene 2.0 ST (Affymetrix) at 45°C for 17 hours.
After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix).
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
|
| Description |
VP16-SOX9∆TAD-ires-GFP transfected EndoC-ßH1 cells
|
| Data processing |
The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls. The observations of some of these metrics and the study of the distribution of raw data show no outlier experiment.
The data were analyzed with R Bioconductor packages using using RMA as normalization method
|
| |
|
| Submission date |
Sep 25, 2017 |
| Last update date |
Jan 31, 2018 |
| Contact name |
Masaya OSHIMA |
| E-mail(s) |
[email protected]
|
| Organization name |
INSERM U1016
|
| Street address |
123 boulevard de Port Royal
|
| City |
Paris |
| ZIP/Postal code |
75012 |
| Country |
France |
| |
|
| Platform ID |
GPL20103 |
| Series (2) |
| GSE104195 |
Expression data from SOX9 overexpressing EndoC-ßH1 cells |
| GSE104196 |
Viral like infection induces Human β cell dedifferentiation |
|
