|
| Status |
Public on Jul 01, 2011 |
| Title |
8071-control |
| Sample type |
RNA |
| |
|
| Source name |
HepG2 hepatocellular carcinoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2 hepatocellular carcinoma cell line
treatment: control
|
| Treatment protocol |
Cells were treated with TCDD at 10nM concentration for 48h
|
| Growth protocol |
Cells were grown in MEM–Eagle (+Earl's BBS), w/NEAA and 10% FBS with additions of sodium bicarbonate and sodium pyruvate.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
EZ-RNA II kit from Biological Industries, Israel, was used for total RNA extraction from cell lines
|
| Label |
Cy3
|
| Label protocol |
Fifteen micrograms of total RNA was labeled by ligation of an RNAlinker p-rCrU-Cy-dye
|
| |
|
| Hybridization protocol |
Labeled RNA was mixed with 33 hybridization buffer (Ambion), heated to 95 C for 3 min, and incubated with the miRdicator array for 12–16 hr
|
| Scan protocol |
Arrays were scanned using Agilent DNA Microarray Scanner Bundle (Agilent Technologies, Santa Clara, CA) at a resolution of 10 mm at 100% power. Array images were analyzed using SpotReader software (Niles Scientific, Portola Valley, CA).
|
| Description |
8071
|
| Data processing |
Triplicate spots were combined to produce one signal for each probe by taking the logarithmic mean of reliable spots. All data were log-transformed (base 2) and the analysis was performed in log-space. A reference data vector for normalization R was calculated by taking the median expression level of a subset of all probes (all miRs in mirbase 10) across samples. For each sample data vector S, a 2nd degree polynomial F was found so as to provide the best fit between the sample data and the reference data, such that R≈F(S). For each probe in the sample (element Si in the vector S), the normalized value (in log-space) Mi was calculated from the initial value Si by transforming it with the polynomial function F, so that Mi=F(Si). P-values were calculated using a two-sided t-test on the log-transformed normalized fluorescence signal. The fold-difference (ratio of the median normalized fluorescence) was calculated for each microRNA.
|
| |
|
| Submission date |
Jul 13, 2010 |
| Last update date |
Jul 01, 2011 |
| Contact name |
Einat Sitbon |
| Organization name |
Rosetta Genomics
|
| Street address |
10 Plaut St
|
| City |
Rehovot |
| ZIP/Postal code |
76706 |
| Country |
Israel |
| |
|
| Platform ID |
GPL10676 |
| Series (2) |
| GSE22909 |
Influence of TCDD onto HCC cell line |
| GSE22910 |
hsa-miR-191, a potential target for Hepatocellular carcinoma therapy |
|
