|
| Status |
Public on Dec 19, 2008 |
| Title |
H187-63AR 1 (565) |
| Sample type |
RNA |
| |
|
| Source name |
lung cancer cell line xenograft
|
| Organism |
Homo sapiens |
| Characteristics |
H187 derivative xenograft
|
| Treatment protocol |
Once the tumors reached >200mm3 the mice were treated with ABT-737 or vehicle control. All the samples shown here were from mice treated with vehicle control.
|
| Growth protocol |
5 million of H187 or H187-63AR cells were injected subcutaneously into nude mice
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from snap frozen tissues using Trizol and purified with RNAeasy columns. RNA quality was assessed using an Agilent 2100 Bioanalyzer. RNA samples were labeled according to the chip manufacturer’s recommended protocols. In brief, 0.5 μg of total RNA from each sample was labeled using the Illumina TotalPrep RNA Amplification Kit in a process of cDNA synthesis and in vitro transcription
|
| Label |
Cy3
|
| Label protocol |
Single stranded RNA was generated and labeled by incorporating biotin-16-UTP.
|
| |
|
| Hybridization protocol |
Hybridized to an Illumina Sentrix Human Ref-8 Expression Beadchip
|
| Scan protocol |
The hybridized biotinylated cRNA was detected with streptavidin-Cy3 and quantitated using an Illumina BeadStation 500GX Genetic Analysis Systems scanner.
|
| Description |
none
|
| Data processing |
Two biological samples from each tumor (H187 and H187-63AR) were hybridized to an Illumina BeadChip. Image level analysis and preprocessing was performed using BeadStudio software (Bead StudioGene Expression Module Users Guide May 2006) according to manufacturers recommendations. The preprocessing algorithm includes outlier detection and produces an average expression value for each oligonucleotide probe sequence. Data analysis and plotting of the expression profiles was done using the R statistical platform and the Bioconductor bioinformatics software project. Pre-processed expression values were transformed to a log scale and averaged over replicates for each of the experimental conditions. Genes having log2 fold changes greater than 1 were used to cluster samples for comparison and presentation.
|
| |
|
| Submission date |
Feb 13, 2008 |
| Last update date |
Feb 13, 2008 |
| Contact name |
Christine Hann |
| Organization name |
Johns Hopkins University School of Medicine
|
| Department |
Oncology
|
| Lab |
Rudin
|
| Street address |
1550 Orleans St., CRB2, Rm 562
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21231 |
| Country |
USA |
| |
|
| Platform ID |
GPL6104 |
| Series (1) |
| GSE10003 |
Gene expression profile of H187-63AR, an ABT-737 resistant derivative of H187 |
|
