|
| Status |
Public on Oct 31, 2011 |
| Title |
HepG2_control_rep_2 |
| Sample type |
RNA |
| |
|
| Source name |
HepG2 cells treated with vehicle for 24 hrs
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2
cell type: hepatoma cells
|
| Treatment protocol |
For the gene expression analysis cells were grown to approximately 60-70% confluence, washed with PBS three times and incubated with DMEM supplemented with 10% TH-depleted serum and treated with vehicle or 10nM ligand (T3 or GC-1).
|
| Growth protocol |
HepG2 cells were grown in Dulbecco's modified Eagle's medium (DMEM)-H21 supplemented with 10% fetal bovine serum (FBS), 100 U/mL of penicillin, 0.1 g/L of streptomycin and 4 mmol/L glutamine, under 95% air and 5% CO2 at 37C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated with acid guanidinium thiocyanate/phenol/chloroform (Chomczynski and Sacchi 1987) by employing TRIZOL® Reagent (Invitrogen, CA) following manufacture’s instruction.RNA integrity was analyzed by Bioanalyzer (Agilent Technologies, Santa Clara, CA) applying Agilent RNA 6000 Nano kit (Agilent). Only samples with 28S/18S rRNA ratio = or ≥ than 1.8 were used.
|
| Label |
biotin
|
| Label protocol |
Biotin-labeled cRNAs were generated from total RNA by using MessageAmp II-Biotin Enhanced Single Round aRNA Amplification Kit (Ambion, TX), incubation time for all in vitro transcription reactions was 14 hours at 37C.
|
| |
|
| Hybridization protocol |
The biotinylated cRNAs were purified and the quality and integrity analyzed by NanoDrop 1000 (Thermo) and Bioanalyzer (Agilent), respectively. Prior to array hybridization, Biotin-cRNA was fragmented by Magnesium-potassium at 94C to generate 35-200 nucleotides cRNA fragments.
|
| Scan protocol |
GeneChips were scanned using Affymetrix gcs3000.
|
| Description |
HepG2 control
|
| Data processing |
CEL files were read into R/Bioconductor using the Affy/affyPLM package (Bolstad et al 2003) and RMA (robust multi-array average) intensity in log2 scale was generated for each probe set.
|
| |
|
| Submission date |
Sep 28, 2011 |
| Last update date |
Oct 31, 2011 |
| Contact name |
Paul Webb |
| E-mail(s) |
PWebb@tmhs.org
|
| Phone |
713-441-2516
|
| Organization name |
Methodist Hospital Reseach Institute
|
| Department |
Diabetes Research Center
|
| Lab |
Genomic Medicine
|
| Street address |
6565 Fannin St. F8-060
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL571 |
| Series (2) |
| GSE32443 |
Identical gene regulation patterns of triiodothyronine (T3) and selective thyroid hormone receptor modulator GC-1 [Affymetrix] |
| GSE32445 |
Identical gene regulation patterns of triiodothyronine (T3) and selective thyroid hormone receptor modulator GC-1 |
|
