|
| Status |
Public on Mar 13, 2014 |
| Title |
N2a-AD-3 |
| Sample type |
RNA |
| |
|
| Source name |
Neuro2a anchorage dependent (AD) cells
|
| Organism |
Mus musculus |
| Characteristics |
background strain: AJ
cell type: neuroblastoma
genotype: anchorage dependent
|
| Treatment protocol |
not applicable.
|
| Growth protocol |
AD cells were cultured in DMEM (Gibco) containing 10% fetal bovine serum (Gibco), 0.5% penicillin/streptomycin (Sigma) and 10% L-glutamine (Sigma). AI cells were grown in NeuroCult complete media consisting of NeuroCult Neural Stem Cell (NSC) Basal medium, 1/10 NeuroCult NSC Proliferation supplements, 20ng/ml EGF, 10ng/ml bFGF and 2µg/ml Heparin (medium, supplements and growth factors all from Stem Cell Technologies).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
All RNA samples from AD and AI cells were prepared using RNeasy kit (Qiagen). The 1st- and 2nd-strand cDNA synthesis, and IVT amplification were performed using the Ambion WT expression kit.
|
| Label |
biotin
|
| Label protocol |
Samples were enzymatically fragmented and biotinylated using the Affymetrix GeneChip WT Terminal Labeling Kit.
|
| |
|
| Hybridization protocol |
Fragmented and biotin-labeled single strand cDNA amples were hybridized using Affymetrix hybridization kit materials. Hyb cocktails were heated at 99° for 5 min, then incubated at 45° for 5 min and centrifuged at max speed for 1 min. The hyb solution (200μl each sample) was then transferred to each arrays. The hybridizations were performed for 16 hours at 45° at 60rpm, and the washing was performed by GeneChip Fluidics Station 450using using Fluidics transcript FS450_0001.
|
| Scan protocol |
Affymetrix GeneChIP Scanner 3000 7G
|
| Description |
Neuro2a anchorage dependent (AD) cells, biological rep 3
|
| Data processing |
Data were processed using Partek Genomics Suite 6.5 program. GCRMA background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities, then quantile normalized and log2 transformed.
|
| |
|
| Submission date |
Mar 14, 2013 |
| Last update date |
Mar 13, 2014 |
| Contact name |
Bi-Dar Wang |
| E-mail(s) |
[email protected]
|
| Phone |
202-994-3543
|
| Fax |
202-994-2870
|
| Organization name |
The George Washington University Medical Center
|
| Department |
Pharmacology and Physiology
|
| Street address |
2300 I street, NW
|
| City |
Washington |
| State/province |
DC |
| ZIP/Postal code |
20037 |
| Country |
USA |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE45160 |
Expression data from Neuro2a mouse neuroblastoma cell lines, anchorage dependent cells (AD) and anchorage-independent tumorspheres (AI) |
|
