|
| Status |
Public on Mar 15, 2015 |
| Title |
HCT116_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
HCT116 cell line, parental, replicate 2
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Cell line, colon cancer derived
cell line: HCT116
treatment: No drug (control parental cell line)
|
| Growth protocol |
Three parental cell lines (HCT116, HT29 and LoVo) were exposed in vitro to gradually increasing concentrations of oxaliplatin or SN-38 for about nine months. Before cell harvest, parental and drug-resistant cell lines were cultured in drug-free growth medium (RPMI1640+Glutamax supplemented with 10% fetal bovine serum, Invitrogen) for two to three weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified from each cell line in independent triplicates (three different passages). Following a wash with cold PBS, TRIzol Reagent (Invitrogen) was added and the cells were lysed on ice. The lysate was frozen at -80˚C for later purification of RNA. RNA was purified according to the manufacturer’s instructions with minor modifications (centrifugation for 4500 x g, with centrifugation times of 20 min for the phase separation and 15 min for the RNA precipitation).
|
| Label |
Cy3
|
| Label protocol |
Total RNA was separately converted into cDNA through reverse transcription, thereafter cRNA was transcribed with T7 RNA Polymerase. Labeled cRNA was coupled to a Cyanine 3-CTP fluorescent dye using the One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling (version 6.5 protocol) (Agilent Technologies).
|
| |
|
| Hybridization protocol |
Cy3-labeled cRNA was hybridized to Agilent Human Gene Expression Microarrays (G4112F).
|
| Scan protocol |
Microarrays were scanned using an Agilent DNA Microarray scanner (Agilent Technologies).
|
| Description |
GE_02
Gene expression of cell line growing in drug-free medium
|
| Data processing |
Microarray data processing was performed in R (www.r-project.org) using the Bioconductor bioinformatics software package (www.bioconductor.org). Data (gProcessedSignals) were loaded into R using the Limma package and normalized between arrays using quantile normalization. Probes were collapsed taking the median and expression values were log2 transformed.
|
| |
|
| Submission date |
Nov 19, 2012 |
| Last update date |
Mar 16, 2015 |
| Contact name |
Niels Frank Jensen |
| Organization name |
University of Copenhagen
|
| Department |
Faculty of Health and Medical Sciences
|
| Lab |
Pathobiology
|
| Street address |
Dyrlaegevej 88, 1.
|
| City |
Frederiksberg C |
| ZIP/Postal code |
1870 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL16297 |
| Series (1) |
| GSE42387 |
Gene expression profiles of parental and chemotherapy-resistant colon cancer cell lines. |
|
