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Chemosensitivity prediction of Paclitaxel-Platinum combination therapy by expression profile in ovarian cancer

ABSTRACT: Ten human ovarian cancer cell lines were kindly provided as follows: an ovarian serous adenocarcinoma cell line, SKOV3 (Dr. N. Nagai, Hiroshima University, Hiroshima, Japan); KF28 and its TXL/CDDP-resistant variant (Dr. Y. Kikuchi, National Defense Medical College, Saitama, Japan); KF, SHIN3 and 5 ovarian clear cell adenocarcinoma cell lines, KK, TAYA, RMG-1, OVISE and OVTOKO (Dr. M. Suzuki, Jichi Medical School, Tochigi, Japan). All cell lines were cultured in RPMI 1640 medium (Life Technologies, Inc., Grand Island, NY) containing 10% heat-inactivated fetal bovine serum (FBS; BioWhittaker, Verviers, Belgium) in a humidified atmosphere of 5% CO2 and maintained in continuous exponential growth by passage every 3 days. Exponentially growing cultured cells were collected after two-washings with PBS. The cell pellets were immediately frozen in liquid nitrogen, and stored until use. Total RNA was extracted using QIAGEN RNeasy mini kit (QIAGEN, Inc., Valencia, CA). The quality of the RNA was checked using Agilent Technologies 2100 Bioanalyzer (Agilent, Palo Alto, CA). CodeLink Expression Bioarray System (Amersham Bioscience, Tokyo, Japan) was used according to the manufacturer’s protocol. Briefly, first-strand cDNA was generated from 1 microgram of total RNA of each cell line using reverse transcriptase and a T7 primer, and then second-strand cDNA was produced using DNA polymerase mix and RNase H. Complementary RNA (cRNA) was generated via an in vitro transcription reaction using T7 RNA polymerase and biotin-11-UTP (Perkin Elmer, Boston, MA), which was quantified by spectrometry and checked using Agilent Technologies 2100 Bioanalyzer (Agilent). Ten-microgram of cRNA was then fragmented and hybridized to a Uniset Human 20K I Bioarray containing 19,881 probes with positive and negative bacterial control probes. After hybridization, the arrays were rinsed and labeled with Streptavidin-Cy5, scanned using Agilent DNA Microarray Scanner (Agilent), then analyzed with CodeLink Expression Analysis Software ver.2.3. Expression levels were normalized to the median expression value of the whole array spots. Keywords: parallel sample

ORGANISM(S): Homo sapiens

PROVIDER: GSE3001 | GEO | 2005/12/31

SECONDARY ACCESSION(S): PRJNA93173

REPOSITORIES: GEO

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Chemosensitivity prediction of Paclitaxel-Platinum combination therapy by expression profile in ovarian cancer

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