|
| Status |
Public on Jun 20, 2014 |
| Title |
UCI-101 cell line, Indomethacin treatment-1 |
| Sample type |
RNA |
| |
|
| Source name |
serous ovarian adenocarcinoma, UCI-101 cell line, 24 hour treatment with Indomethacin.
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: serous ovarian adenocarcinoma, UCI-101 cell line.
growth protocol: The serous ovarian adenocarcinoma cell line UCI-101 was cultured in McCoy’s 5A culture media supplemented with 10% fetal bovine serum and Pen/Strep (100 units/mL penicillin and 100 mg/mL streptomycin). Cells were incubated at 37°C in an atmosphere of 5% CO2. All experiments were performed in serum-containing media.
treatment: UCI-101 cell lines were seeded in 60 mm dishes and treated for 24 hours with 300 mM diclofenac or indomethacin.
|
| Treatment protocol |
Serous ovarian adenocarcinoma cell lines were seeded in 60 mm dishes and treated for 24 hours with nothing or 300 mM of either diclofenac or indomethacin.
|
| Growth protocol |
The serous ovarian adenocarcinoma cell lines HEY, OVCAR5 and UCI-101 were cultured in McCoy’s 5A culture media supplemented with 10% fetal bovine serum and Pen/Strep (100 units/mL penicillin and 100 mg/mL streptomycin). Cells were incubated at 37°C in an atmosphere of 5% CO2. All experiments were performed in serum-containing media.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
24 hours after treatment total RNA was prepared using the Qiagen RNeasy Mini Kit (Qiagen, Inc. Valencia CA) following the manufacturer's specifications. Quantity and quality of the RNA was assessed using the Agilent 2100 Bioanalyzer with 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, 0.5ug 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 v2.0 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has ~24,000 well-annotated RefSeq transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the biotin 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 |
serous ovarian adenocarcinoma, UCI-101 cell line, 24 hour treatment with Indomethacin.
|
| Data processing |
Data was extracted using the Illumina BeadStudio software(v3.1.7). Any spots at or below the background were filtered out using an Illumina detection p value of 0.02 and above. 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.
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| |
|
| Submission date |
Mar 12, 2013 |
| 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) |
| GSE45052 |
Non-steroidal Anti-inflammatory Drugs Decrease E2F1 Expression and Inhibit Cell Growth in Ovarian Cancer Cells |
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