|
| Status |
Public on Dec 31, 2015 |
| Title |
SK-N-BE(2) treated for 8h with 1 uM compound 8148_30880 |
| Sample type |
RNA |
| |
|
| Source name |
SK-N-BE(2)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SK-N-BE(2)
treatment: 8148
|
| Treatment protocol |
SK-N-BE(2) cells were incubated with compound 8 h. DMSO was used as negative control.
|
| Growth protocol |
Neuroblastoma SK-N-BE(2) cells (ATCC CRL-2271) were cultured using a modified 1:1 mixture of Dulbecco's Modified Eagle's Medium and F12 Medium, DMEM/HAMF12 (Composition: 500 ml DMEM/HAMF12 (31331), 28 ml FBS (heat inactivated, New Zealand origin), 5 ml SOL B, 5.7 ml NEAA, 8.5 ml HEPES, 5.7 ml L-Glutamine)., complemented with fetal bovine serum to a final concentration of 5%. Cells were grown in 175cm² culture flasks at 37°C under 5% CO2 and split at 80% confluence every 3 to 4 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed using RLT buffer (Qiagen) and RNA extracted with the RNeasy 96 kit (p/n 74181 Qiagen).
|
| Label |
biotin
|
| Label protocol |
All microarray related steps for target preparation including amplification of total RNA and labeling were carried out as described in the GeneChip®3’ IVT, Express Kit User Manual , (Affymetrix 2004).
|
| |
|
| Hybridization protocol |
Target hybridization was processed on the GeneTitan® Instrument according to the instructions provided in the User Guide for Expression Array Plates (P/N 702933).
|
| Scan protocol |
Plate scan was processed on the GeneTitan® Instrument according to the instructions provided in the User Guide for Expression Array Plates (P/N 702933). Images were analyzed using the GeneChip® Command Console Software (AGCC), (Affymetrix).
|
| Data processing |
The data were analyzed using R 3.0.1, affy package version 1.34.0 & 1.38.1, farms package version 1.12.0 and Entrez based alternative CDF version 15.1.0 for probeset annotation
|
| |
|
| Submission date |
Jul 07, 2015 |
| Last update date |
Dec 31, 2015 |
| Contact name |
Steven Osselaer |
| E-mail(s) |
[email protected]
|
| Organization name |
Janssen Pharmaceutica NV
|
| Street address |
Turnhoutseweg 30
|
| City |
Beerse |
| ZIP/Postal code |
2340 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL19100 |
| Series (2) |
| GSE70614 |
Integrating high-dimensional transcriptomics and image analysis tools into early safety screening (III) |
| GSE70617 |
Integrating high-dimensional transcriptomics and image analysis tools into early safety screening |
|
