Comment[ArrayExpressAccession] E-MTAB-1661
MAGE-TAB Version 1.1
Investigation Title Mixed-polarization phenotype of ascites-associated macrophagesin human ovarian carcinoma: correlation of CD163 expression, cytokine levels and early relapse
Comment[Submitted Name] Mixed-polarization phenotype of ascites-associated macrophagesin human ovarian carcinoma: correlation of CD163 expression, cytokine levels and early relapse
Experiment Description Ascites-associated macrophages were collected from human ovarian carcinoma patients and their expression profiles determined via Agilent microarrays. In addition, monocyte derived macrophages from healthy donors were differentiated ex-vivo with MCSF and GMCSF and their expression profiles determined as well.
Experimental Design cell_type_comparison_design disease_state_design ex_vivo_design in_vivo_design reference_design co-expression_design compound_treatment_design
Comment[AEExperimentType] transcription profiling by array
Comment[AEExperimentDisplayName] Transcription profiling by array of ascites-associated macrophages from human ovarian carcinoma patients and monocyte-derived macrophages from healthy donors differentiated ex-vivo with MCSF and GMCSF
Quality Control Type
Experimental Factor Name compound dose disease state cell type
Experimental Factor Type compound dose disease state cell type
Public Release Date 2014-03-07
Person Phone +49 6421 2825337 +49 6421 5866417 +49 6421 2865375 +49 6421 2865026 +49 6421 2863707 +49 6421 2866236
Person Email finkernagel@imt.uni-marburg.de reinartz@med.uni-marburg.de schumann.tim@imt.uni-marburg.de meissner@imt.uni-marburg.de krausemi@staff.uni-marburg.de rmueller@imt.uni-marburg.de
Person Roles submitter;investigator investigator investigator investigator investigator investigator
Person Affiliation Institute for Molecular Biology and Tumor Research Clinic for Gynecology, Gynecological Oncology and Gynecological Endocrinology, Philipps University Institute for Molecular Biology and Tumor Research Institute for Molecular Biology and Tumor Research Institute for Molecular Biology and Tumor Research Institute for Molecular Biology and Tumor Research
Person Address Emil-Mannkopff Str. 2, D-35032 Marburg, Germany Baldingerstraße, D-35033 Marburg, Germany Emil-Mannkopff Str. 2, D-35032 Marburg, Germany Emil-Mannkopff Str. 2, D-35032 Marburg, Germany Emil-Mannkopff Str. 2, D-35032 Marburg, Germany Emil-Mannkopff Str. 2, D-35032 Marburg, Germany
Person Last Name Finkernagel Reinartz Schumann Meissner Krause Mueller
Person Mid Initials
Person First Name Florian Silke Tim Wolfgang Michael Rolf
Protocol Name P-MTAB-32735 P-MTAB-32736 P-MTAB-32737 P-MTAB-32738 P-MTAB-32739 P-MTAB-32740 P-MTAB-32741 P-MTAB-32742 P-MTAB-32743
Protocol Type growth protocol treatment protocol nucleic acid extraction protocol pool nucleic acid labeling protocol nucleic acid hybridization to array protocol array scanning and feature extraction protocol normalization data transformation protocol normalization data transformation protocol
Protocol Description Ascites was collected from patients with high grade serous ovarian carcinoma undergoing primary surgery at the University Hospital in Marburg. Informed consent was obtained from all patients according to the protocols approved by the local ethical committee. Peripheral blood mono-nuclear cells (PBMC) were obtained from healthy adult volunteers for monocyte-derived macrophage (MDM) stimulation. Mononuclear cells were isolated from ascites and peripheral blood by ficoll (GE Heathcare/PAA, Cölbe, Germany) density gradient centrifugation and further purified by magnetic cell sorting (MACS) using CD14 microbeads (Miltenyi Biotech, Bergisch Gladbach, Germany). Purified TAMs and MDMs were directly analyzed by FACS, lysed in PeqGold (Peqlab, Erlangen, Germany) for RNA preparation or cultured in serum-free macrophage medium (Mph medium; Life Technologies, Darmstadt, Germany). CD14+ monocytes and TAMs were cultured in serum-free macrophage medium (Mph medium; Life Technologies, Darmstadt, Germany). Monocyte-derived macrophages (MDMs) were differentiated from CD14+ monocytes of healthy volunteers for 5-7 d at 1x106 cells/ml in Mph medium supplemented with either MCSF or GMCSF or DMSO control (Immunotools, Friesoythe, Germany). RNA was isolated using the Nucleospin RNA II kit (Macherey-Nagel, Dueren, Germany) according to manufacturers instructions. A equal aliquot of Cy3 labeled extracts from samples TAM 21, TAM 23, TAM 22, TAM 29 was pooled to build a reference. Title: Agilent Two-Color Microarray-Based Gene Expression (Quick Amp Labeling). Description: Agilent Two-Color Microarray-Based Gene Expression (Quick Amp Labeling)
Version: 5.7
Agilent publication number: G4140-90050
URL: http://www.chem.agilent.com/Library/usermanuals/Public/G4140-90050_Two-Color_GE_5.7.pdf
This document describes Agilent's recommended procedures for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for microarray-based two-color gene expression analysis. Title: Agilent Two-Color Microarray-Based Gene Expression (Hybridization). Description: Agilent Two-Color Microarray-Based Gene Expression (Hybridization)
Version: 5.7
Agilent publication number: G4140-90050
URL: http://www.chem.agilent.com/Library/usermanuals/Public/G4140-90050_Two-Color_GE_5.7.pdf
This document describes Agilent's recommended procedures for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for microarray-based two-color gene expression analysis. Slides were scanned using an Agilent DNA Microarray Scanner G2505C; scan software: Agilent Scan Control Version A.8.1.3; quantification software: Agilent Feature Extraction Version 10.5.1.1 (FE Protocol GE_105_Dec08).(Parameters: Scanning hardware = G2505A DNA microarray scanner [Agilent], Scanning software = Feature Extraction Software [Agilent]) Data was log2 transformed Data was background substracted and LOESS normalized within arrays and scale normalized between arrays using R (2.15)/Bioconductor/Limma
Protocol Term Source REF EFO EFO EFO EFO EFO EFO EFO EFO EFO
Term Source Name EFO
Term Source File http://www.ebi.ac.uk/efo
SDRF File E-MTAB-1661.sdrf.txt
PubMed ID 23784932
Publication Author List Reinartz S, Schumann T, Finkernagel F, Wortmann A, Jansen JM, Meissner W, Krause M, Schworer AM, Wagner U, Muller-Brusselbach S, Muller R.
Publication Title Mixed-polarization phenotype of ascites-associated macrophages in human ovarian carcinoma: correlation of CD163 expression, cytokine levels and early relapse.
Publication DOI 10.1002/ijc.28335