|
| Status |
Public on Jun 12, 2017 |
| Title |
control 3 |
| Sample type |
RNA |
| |
|
| Source name |
control
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SH-SY5Y
cell type: neuroblastoma
treatment: control
|
| Treatment protocol |
Three samples of SH-SY5Y cells and four samples of 72h treated SH-SY5Y neuroblastoma cell line with 10µM CDDP for 72h were subjected to Affymetrix chip analyses.
|
| Growth protocol |
The SH-SY5Y (ATCC® CRL2266™), neuroblastoma cell line was obtained from American Type Culture Collection (ATCC, Manassas, Virginia). The cells were maintained in culture as recommended by the provider. SH-SY5Y cells were grown in DMEM/F12 medium supplemented with 10% (v/v) heat inactivated fetal bovine se-rum (FBS), penicillin (0.1lU) and streptomycin (100μg/mL). The cells were cultured under sterile conditions and were grown in a humidified incubator at 37°C with 95% O2 and 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For extraction of RNA and DNA we used the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) following the provider’s protocol. Extracted RNA was kept at -80°C.
|
| Label |
Biotin
|
| Label protocol |
RNA quality was determined using the Agilent Bioanalyzer and the Eukaryote Total RNA Nano Chip (Agilent Technologies, Hayward, CA, USA). The RNA integrity number (RIN) was measured as 9.9-10. The Affymetrix HuGene 2.0 ST and WT plus reagent kit (Affymetrix, Santa Clara, California, United States) was used following the provider’s recommendation with a start material of 100ng of total RNA.
|
| |
|
| Hybridization protocol |
Affymetrix chip hybridizations were performed at the Center for Biological and Medical Research (BMFZ) at Heinrich Heine University Düsseldorf using a GeneChip Hybridization Oven 645 and a GeneChip® Scanner 3000 7G.
|
| Scan protocol |
GeneChip® Scanner 3000 7G
|
| Data processing |
Bioinformatic evaluation of the microarray data was done with the R framework for statistical computing. The dataset was normalized and log2-transformed using the robust multi-array average (RMA) method implemented in the affy package. Differential expression of mRNA was assessed by computing the moderated t-statistics using the LIMMA package. The resulting p-values were corrected for multiple testing by controlling the false discovery rate. An mRNA was considered as being differentially expressed when the corrected p-value was below 0.05.
|
| |
|
| Submission date |
Sep 12, 2016 |
| Last update date |
Jun 12, 2017 |
| Contact name |
Ana-Maria Florea |
| E-mail(s) |
anamflorea@gmail.com
|
| Phone |
+491797776429
|
| Organization name |
University Düsseldorf
|
| Department |
Neuropathology
|
| Lab |
Ana-Maria Florea
|
| Street address |
Moorenstr. 5
|
| City |
Düsseldorf |
| State/province |
NRW |
| ZIP/Postal code |
40225 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16686 |
| Series (1) |
| GSE86842 |
Changes in gene expression upon treatment of SH-SY5Y cells to cisplatin |
|
