|
| Status |
Public on Mar 12, 2012 |
| Title |
OV90 P3 1 |
| Sample type |
RNA |
| |
|
| Source name |
The ovarian cancer cell line OV90 was obtained from The American Type Culture Collection (ATCC)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: ovarian cancer cell
cell line: OV90
resistance type: paclitaxel resistant sub-line of OV90 was generated by exposure to the chemotherapeutic drug (Sigma) for four cycles. For each cycle, the cells were exposed to the drug for twenty-four hours, and then transferred to normal media where they were allowed to grow for 2 weeks. Following this two-week period, the cells were re-exposed to the drug to initiate the next cycle for a total of 6 cycles. Subclones were isolated and expanded after the last cycle.
|
| Treatment protocol |
Cells were grown in 1:1 mixture of MCDB 105 medium (Sigma) and Medium 199 (Invitrogen) containing 15% bovine serum and antibiotics (100 units/ml penicillin and 100 ug/ml streptomycin) at 37°C in a humidified atmosphere of 5% CO2, these untreated cells were then harvested for RNA preparation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from the treated cells using Trizol. Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.
|
| Label |
Streptavidin-Cy3 bound to biotin-labeled cRNA.
|
| Label protocol |
standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5g of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.
|
| |
|
| Hybridization protocol |
standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Sentrix Human Ref-8 v2 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has ~22,000 transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the labeled cRNA was detected by staining with streptavidin-Cy3.
|
| Scan protocol |
Arrays were scanned at a resolution of 0.8um using the Beadstation 500 X from Illumina.
|
| Description |
This paclitaxel resistant sub-line of OV90 was generated by exposure to the chemotherapeutic drug (Sigma) for four cycles. For each cycle, the cells were exposed to the drug for twenty-four hours, and then transferred to normal media where they were allowed to grow for 2 weeks. Following this two-week period, the cells were re-exposed to the drug to initiate the next cycle for a total of 6 cycles. Subclones were isolated and expanded after the last cycle.
OV90 P3 1
|
| Data processing |
Data was extracted using the Illumina BeadStudio software(v1.5.0.34). Any spots at or below the background were filtered out using an Illumina detection value below 0.98. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below. Z-score = (raw value - avg)/std. Complete data including detection scores will be included in the supplemental file.
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| |
|
| Submission date |
Jan 05, 2011 |
| Last update date |
Jun 22, 2020 |
| Contact name |
Supriyo De |
| Organization name |
NIA-IRP, NIH
|
| Department |
Laboratory of Genetics and Genomics
|
| Lab |
Computational Biology & Genomics Core
|
| Street address |
251 Bayview Blvd
|
| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21224 |
| Country |
USA |
| |
|
| Platform ID |
GPL6104 |
| Series (1) |
| GSE26465 |
Beta-microseminoprotein (MSMB) downregulation is associated with increased drug resistance in ovarian cancer |
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