|
| Status |
Public on Sep 05, 2014 |
| Title |
NT_siRNA_YCC3_1 |
| Sample type |
RNA |
| |
|
| Source name |
NT_siRNA_YCC3
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: YCC3
cell type: gastric cancer
|
| Treatment protocol |
NA
|
| Growth protocol |
YCC3 cell lines were grown in MEM/10%FBS/ 1X NEAA/ 1X L-glutamine/ Pen-strep. AGS and KATOIII cell lines grown in RPMI 1640/10%FBS/ 1X NEAA/ 1X L-glutamine/ Pen-strep. They are cultured at 37 °C with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted, DNAse treated, and purified using a RNAeasy Mini Kit (Qiagen). Reverse transcription to obtain cDNAs were performed using SuperScript III Kits (Life Technologies).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according the Attymetrix protocol from 250ng of total RNA (GeneChip® 3’ IVT Express Kit User Manual, 2008, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 12.5ug of cRNA were hybridized on the Affymetrix Human Genome U133 plus Genechips (HG-U133 Plus 2.0, Affymetrix) for 16hr at 45oC.
|
| Scan protocol |
GeneChips were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix) and scanned using the GeneChip Scanner 3000 7G (Affymetrix)
|
| Description |
NA
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using R/bioconductor affy package
|
| |
|
| Submission date |
Oct 25, 2013 |
| Last update date |
Sep 05, 2014 |
| Contact name |
Niantao Deng |
| Organization name |
Duke NUS Graduate Medical School
|
| Street address |
Center for Computational Biology, level 6, 8 College Road
|
| City |
Singapore |
| State/province |
Singapore |
| ZIP/Postal code |
169857 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL570 |
| Series (2) |
| GSE51704 |
Gene expression profiling of KLF5, GATA4 and GATA6 knock down in YCC3/AGS/KATOIII cell lines |
| GSE51706 |
Integrative study of cooperative lineage-survival oncogenes in gastric cancer |
|
