|
| Status |
Public on Nov 25, 2015 |
| Title |
Control shRNA biological replicate 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Control shRNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: GBM6840
treatment: Control shRNA
|
| Treatment protocol |
Cells were transduced with a control or chronophin targeting shRNA. For rescue experiments, an RNAi-resistant human chronophin was expressed
|
| Growth protocol |
human glioma cells (GBM6840) were cultured in DMEM supplemented with 10 % FCS, 2mM L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin, 1 µg/ml puromycin and 400 µg/ml G418
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the SV Total RNA Isolation System following the manufacturers´s instructions
|
| Label |
Cy5
|
| Label protocol |
Agilent Two-Color Microarray-Based Gene Expression (Quick Amp Labeling) Version: 5.7 Agilent publication number: G4140-90050
|
| |
|
| Channel 2 |
| Source name |
reference: pool of all samples
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: GBM6840
|
| Treatment protocol |
Cells were transduced with a control or chronophin targeting shRNA. For rescue experiments, an RNAi-resistant human chronophin was expressed
|
| Growth protocol |
human glioma cells (GBM6840) were cultured in DMEM supplemented with 10 % FCS, 2mM L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin, 1 µg/ml puromycin and 400 µg/ml G418
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the SV Total RNA Isolation System following the manufacturers´s instructions
|
| Label |
Cy3
|
| Label protocol |
Agilent Two-Color Microarray-Based Gene Expression (Quick Amp Labeling) Version: 5.7 Agilent publication number: G4140-90050
|
| |
|
| |
| Hybridization protocol |
gilent hybridization protocol
|
| Scan protocol |
Slides were scanned using an Agilent DNA Microarray Scanner G2505C; scan software: Agilent Scan Control Version A.8.1.3
|
| Data processing |
Agilent Feature Extraction Version 10.5.1.1 (FE Protocol GE_105_Dec08).(Parameters: Scanning hardware = G2505A DNA microarray scanner [Agilent], Scanning software = Feature Extraction Software [Agilent])
The Limma package was used to normalize the expression log-values (M-Values) within each array using the LOESS method. Intensity values (A-values) were normalized between arrays by quantile normalization, using the Aquantile method
|
| |
|
| Submission date |
Aug 06, 2015 |
| Last update date |
Nov 25, 2015 |
| Contact name |
Markus Schulze |
| E-mail(s) |
[email protected]
|
| Organization name |
University Hospital Regensburg
|
| Department |
Neuropathology
|
| Lab |
Markus Riemenschneider
|
| Street address |
Franz-Josef-Strauss Allee 11
|
| City |
Regensburg |
| ZIP/Postal code |
93053 |
| Country |
Germany |
| |
|
| Platform ID |
GPL10332 |
| Series (1) |
| GSE71786 |
Human glioma cells: chronophin (CIN/PDXP) knockdown vs. control or rescue |
|
