|
| Status |
Public on Jan 16, 2009 |
| Title |
HeLa_siGFP_48_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
HeLa total RNA, 48hrs after transfection of siRNA against GFP
|
| Organism |
Homo sapiens |
| Characteristics |
Cervical cancer cell line
|
| Treatment protocol |
32nM of siRNAs (Samchully Phamaceuticals) were transfected into HeLa cells with lipofectamine 2000 (InvitroGen).
|
| Growth protocol |
HeLa cells were cultured in DMEM supplemented with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Wt_sensetarget_label_manual(updated manual)_1, 2007, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 2.3 ug of cDNA were hybridized for 17 hr at 45C on GeneChip Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. Hybridization cocktails containing 5 to 5.5 µg of fragmented, end-labeled single-stranded cDNA were prepared and hybridized to GeneChip Human gene 1.0 ST arrays
|
| Scan protocol |
GeneChips were scanned using the GeneChip Scanner 3000 7G.
|
| Description |
Expression changes of HeLa mRNA after GFP knockdown for 48hrs
|
| Data processing |
All gene array data was analyzed using tools in Expression consol software (Affymetrix). The Robust Multi-array Analysis (RMA) (Irizarry, Hobbs, Collin, Beazer-Barclay, Antonellis, Scherf, and Speed 2003) algorithm was used for probeset (gene-level) intensity analysis.
|
| |
|
| Submission date |
Nov 18, 2008 |
| Last update date |
Jan 16, 2009 |
| Contact name |
Jinju Han |
| Organization name |
Seoul National University
|
| Lab |
Bd. 504, Rm 501
|
| Street address |
599 Gwanangno, Gwanak-gu
|
| City |
Seoul |
| ZIP/Postal code |
151-742 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL6244 |
| Series (2) |
| GSE13638 |
Ago2 or Dicer knockdown effects on mRNA levels in HeLa |
| GSE13640 |
Effect of miRNA biogenesis factors on mRNA levels |
|
