|
| Status |
Public on Dec 02, 2013 |
| Title |
TUM D15 EVE 3 |
| Sample type |
RNA |
| |
|
| Source name |
TUM D15 EVE
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U87
cell type: human glioma
host: chick CAM (chorioallantoic membranne)
|
| Growth protocol |
U87 human glioma cells were cultured in DMEM with 10% FBS, antibiotics and L-glutamine. Fertilised chicken eggs were kept and prepared as described in (Hagedorn, M et al. 2002. PMID: 12460903)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Qiagen (Valencia, CA) RNeasy columns
|
| Label |
Cy3
|
| Label protocol |
RNA was reverse transcribed (cDNA Synthesis System Kit, Roche Diagnostics), purified and transcribed in the presence of Cy3 and Cy5 labels (Megascript D7 Kit, Ambion, Austin, TX).
|
| |
|
| Hybridization protocol |
RNA was hybridised to Agilent Chicken V1 microarrays (for stroma and CAM) and Human GE v2 microarrays (for tumour) (Agilent Technologies, CA). Due to the proximity of tumour cells to the surrounding chicken cells no attempt was made to separate them, instead pooled RNA from both types of cell were hybridised to chicken and human arrays. CAM cells distant from the tumour were hybridised to chicken arrays.
|
| Scan protocol |
Scanning and spot analysis were done according to the manufacturer’s instructions.
|
| Data processing |
Controls were removed from the data after scanning. The arrays were log2 transformed and normalised using between arrays quantile normalisation in the R software package preprocessCore from BioConductor
|
| |
|
| Submission date |
Jan 23, 2013 |
| Last update date |
Dec 02, 2013 |
| Contact name |
Nil Turan |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Birmingham
|
| Street address |
University of Birmingham, Edgbaston
|
| City |
Birmingham |
| ZIP/Postal code |
B15 2TT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL4133 |
| Series (1) |
| GSE43674 |
U87 cells implanted on a chick CAM (Chorioallantoic Membrane) |
|
