|
| Status |
Public on Sep 11, 2015 |
| Title |
cell line_Control_12h_1 |
| Sample type |
RNA |
| |
|
| Source name |
cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Hela cell line
|
| Treatment protocol |
After 24 h stabilization period, cells were treated with the RuT7 complex and CDDP at concentrations equal to 0.5 x IC50. Control samples were left untreated. Following 12 and 24 h, cells were harvested by trypsinization, washed by ice cold PBS and cell pellet was collected by centrifugation at 2000 rpm, 10 min at 4 ˚C and frozen at -80 ˚C.
|
| Growth protocol |
1 x 106 and 0.7 x 106 HeLa cells/25 cm2 falcon dish were seeded (Thermo Scientific Nunc™) for 12 and 24 h treatment, respectively.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from frozen cell pellets using Trizol reagent (Invitrogen) and RNA cleanup was performed using RNeasy Mini Kit (QIAGEN). RNA quantity and quality was estimated using BioSpec Nano (Shimadzu Scientific Instruments) and 1% agarose gel electrophoresis.
|
| Label |
Cy3
|
| Label protocol |
100 ng of total RNA was amplified and labeled with Cyanine-3 (Cy3) fluorescent dye using Low Input Quick Amp Labeling Kit (Agilent Technologies). Fluorescently labeled samples were purified using QIAGEN’s RNeasy Mini spin columns and eluted in 30 µl of nuclease-free water, and cRNA quantity and Cy3 incorporation level was determined using BioSpec Nano (Shimadzu Scientific Instruments).
|
| |
|
| Hybridization protocol |
For each sample 600 ng of Cy3-labelled cRNA was mixed, fragmented for 1 h at 60 ⁰C for 30 min and hybridized at 65 ⁰C for 17 h.
|
| Scan protocol |
microarray slides were washed according to protocol provided by the manufacturer and scanned using Agilent SureScan Microarray Scanner (Agilent Technologies, Santa Clara, CA, USA). Images were processed using Agilent Feature Extraction v.11 software.
|
| Description |
Gene expression after 12h in Control treated Hela cell line
|
| Data processing |
Raw data files were imported in Agilent GeneSpring, flagged probes and control probes were filtered out and background corrected data was normalized by scaling to 75th percentile and log 2 transformed. Probes where at least 70.0 percent of samples have flags and low expressed probes (bottom 20 %) were filtered out, retaining 41929 probes.
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| |
|
| Submission date |
Sep 10, 2015 |
| Last update date |
Sep 11, 2015 |
| Contact name |
Miljana Tanic |
| E-mail(s) |
tanic.miljana@gmail.com
|
| Organization name |
Institute for Oncology and Radiology of Serbia (IORS)
|
| Department |
Experimental Oncology
|
| Lab |
Laboratory of Molecular Genetics
|
| Street address |
Pasterova 14
|
| City |
Belgrade |
| ZIP/Postal code |
11000 |
| Country |
Serbia |
| |
|
| Platform ID |
GPL13607 |
| Series (1) |
| GSE72905 |
Cellular and molecular response to ruthenium(II)-arene complex with substituted picolinato ligand in HeLa cells |
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