Comment[ArrayExpressAccession]	E-MTAB-1858
MAGE-TAB Version	1.1
Investigation Title	Transcription profiling of xenografted tumors derived from human ovarian cell line model A2780 and its cisplatin resistant variant A2780cis
Comment[Submitted Name]	Transcription profiling of xenografted tumors derived from human ovarian cell line model A2780 and its cisplatin resistant variant A2780cis
Experiment Description	Molecular mechanisms underlying the development of resistance to platinum treatment in patients with ovarian cancer remain poorly understood. This is mainly due to the lack of appropriate in vivo models allowing identification of factors that are regulated during initial treatment and of acquired resistance-related genes. In this study, we used whole genome microarrays and linear model analysis to identify potential resistance-related genes by comparing the expression profiles of the parental human ovarian cancer model A2780 and its cisplatin-resistant variant A2780cis, before and after carboplatin treatment in vivo.
Experimental Design	compound treatment design	all pairs	co-expression_design	in_vitro_design
Comment[AEExperimentType]	transcription profiling by array
Comment[AEExperimentDisplayName]	Transcription profiling by array of xenografted tumors derived from human ovarian cell line model A2780 and its cisplatin resistant variant A2780cis
Experimental Factor Name	dose	compound	clinical information
Experimental Factor Type	dose	compound	clinical information
Quality Control Type	biological replicate
Quality Control Term Source REF	EFO
Public Release Date	2013-10-01
Person Last Name	Meier
Person First Name	Julia
Person Mid Initials	C.
Person Email	julia.meier412@gmail.com
Person Phone
Person Address	Bayer Pharma AG, Muellerstr. 178, 13353 Berlin, Germany
Person Affiliation	Bayer Pharma AG
Person Roles	submitter
PubMed ID
Publication Author List	Julia C. Meier, Bernard Haendler, Henrik Seidel, Philip Groth, Robert Adams, Karl Ziegelbauer, Bertolt Kreft, Georg Beckmann, Anette Sommer and Charlotte Kopitz
Publication Title	Knockdown of platinum-induced growth differentiation factor 15 (GDF15) abrogates p27-mediated tumor growth delay in the chemoresistant ovarian cancer model A2780cis in vivo
Publication Status	in preparation
Protocol Name	P-MTAB-34523	P-MTAB-34524	P-MTAB-34525	P-MTAB-34526	P-MTAB-34527	P-MTAB-34528
Protocol Type	growth protocol	treatment protocol	nucleic acid extraction protocol	nucleic acid labeling protocol	nucleic acid hybridization to array protocol	array scanning protocol
Protocol Description	Female fox-chase SCID mice (CBd17/ctrl), 5M-^V6 weeks old (Charles River Laboratories) were injected subcutaneously with 0.5 x 106 A2780 or A2780cis cells in 100% BD MatrigelTM (BD Biosciences), into the right flank. Body weight and tumor area (length x width) were assessed at least twice weekly. Tumors were allowed to grow up to >50 mmM-2 . Animal experiments were conducted in accordance with the German animal welfare law, approved by local authorities and in accordance with the ethical guidelines of Bayer AG. 	For short-term carboplatin treatment, mice were randomly assigned to experimental groups and intravenous (i.v.) treatments using tail vein injection were started (75 mg/kg carboplatin (Q1Dx2)). Control mice received equal volumes and schedules of vehicle alone (0.9% NaCl). 24 h after last treatment (short-term study) or when tumors reached ~150mmM-2 (long-term study), respectively, mice were sacrificed, tumors obtained, weighted, bisected and either snap-frozen for RNA. 	A2780 and A2780cis short-term carboplatin- and vehicle-treated bisected tumors (minimal size 30 mg, n=4-5) were homogenized, RNA was isolated with RNeasy kit (Qiagen) and quality-controlled with RNA NanoChips (Agilent Technologies) at RIN greater than or = 8-10 (RNA integrity number) according to the manufacturerM-4s instructions. 	RNA labeling was performed on a Hamilton Star Roboter (Hamilton, Bonaduz, Switzerland) using the Illumina Total Prep-96 RNA Amplification kit from Ambion (Applied Biosystems, #4393543). Briefly, from 500 ng total RNA first and second strand cDNA was synthesized, and cDNA was cleaned-up using Agencourt magnetic beads CleanKit (#000494, Beckman Coulter). After in vitro transcription, biotin-labeled cRNA was purified using Agencourt magnetic beads CleanKit. cRNA concentration was determined with Quant-iT RiboGreen (R-11490, Invitrogen). 	Little dipper: 1.5 ug cRNA was mixed with the hybridization reagents and hybridized to Illumina Human HT-12 v3 BeadChips. All washing and staining steps were performed with a Little Dipper Processor for Illumina BeadChips from Scigene (Sunnyvale, USA). Biotin was labeled with streptavidin-Cy3 (#PA43001, Amersham Biosciences). 	The BeadChips were  scanned on an Illumina BeadArray Reader.
Protocol Term Source REF	EFO	EFO	EFO	EFO	EFO	EFO
Term Source Name	EFO
Term Source File	http://www.ebi.ac.uk/efo
SDRF File	E-MTAB-1858.sdrf.txt