Genomes and Genes
Affiliation: University of Heidelberg
- Targeting mitosis-regulating genes in cisplatin-sensitive and -resistant melanoma cells: A live-cell RNAi screen displays differential nucleus-derived phenotypesHolger Erfle
BIOQUANT, Heidelberg University, Heidelberg, Germany
Biotechnol J 10:1467-77. 2015..We hereby show that siRNA screening may help to identify tumor-specific genes leading to phenotype abnormalities. These genes may serve as potential therapeutic targets in the treatment of melanoma. ..
- Cell arrays and high-content screeningHolger Erfle
BIOQUANT, University of Heidelberg, Heidelberg, Germany
Methods Mol Biol 785:277-87. 2011..The approach can be modified to quantify endocytosis of other cargo, and can be used under the conditions of knock-down and knock-in as well as for chemical screening...
- Work flow for multiplexing siRNA assays by solid-phase reverse transfection in multiwell platesHolger Erfle
Cell Biology Biophysics Unit, EMBL, Heidelberg, Germany
J Biomol Screen 13:575-80. 2008..We conclude that solid-phase reverse transfection in multiwell plates is a cost-efficient and flexible tool for multiplexing cellular assays...
- Cell arrays for the measurement of organelle dynamics in living cellsHolger Erfle
BIOQUANT, University of Heidelberg, Heidelberg, Germany
Methods Mol Biol 706:73-81. 2011..The approach can be applied for large-scale RNA interference studies as well as for chemical screening...
- Normalizing for individual cell population context in the analysis of high-content cellular screensBettina Knapp
Heidelberg University, Viroquant Research Group Modeling, Bioquant BQ26, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
BMC Bioinformatics 12:485. 2011..However, standard analysis methods for cellular screens do not currently take individual cell data into account unless this is important for the phenotype of interest, i.e. when studying cell morphology...
- miR-17-5p regulates endocytic trafficking through targeting TBC1D2/ArmusAndrius Serva
BIOQUANT, University of Heidelberg, Heidelberg, Germany
PLoS ONE 7:e52555. 2012..Our study reveals regulation of endocytic trafficking as a novel function of miR-17, which might act cooperatively with other functions of miR-17 and related miRNAs in health and disease...
- Live-cell assays to identify regulators of ER-to-Golgi traffickingTautvydas Lisauskas
BIOQUANT, University of Heidelberg, 69120, Heidelberg, Germany
Traffic 13:416-32. 2012..Moreover, we show that our assays can be extended to RNAi and chemical screens...
- Reverse transfection on cell arrays for high content screening microscopyHolger Erfle
MitoCheck Project Group, EMBL, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
Nat Protoc 2:392-9. 2007..Different human cell lines that have been successfully transfected using the protocol are presented here. The present protocol has been applied to two genome-wide siRNA screens addressing mitosis and constitutive protein secretion...
- Measuring secretory membrane traffic: a quantitative fluorescence microscopy approachVytaute Starkuviene
University of Heidelberg, Heidelberg, Germany
Methods Mol Biol 457:193-201. 2008..For each assay the authors discuss protocols for sample preparation, parameters for automated image acquisition, strategies of image analysis, and data quantification...
- Arrays of transfected mammalian cells for high content screening microscopyHolger Erfle
Cell Biology and Cell Biophysics Program, European Molecular Biology Laboratory, Heidelberg, Germany
Methods Enzymol 404:1-8. 2005..The method is suitable for high content screening microscopy at a high spatial and temporal resolution allowing even time-lapse analysis of hundreds of samples in parallel...
- Next-generation 9216-microwell cell arrays for high-content screening microscopyJürgen Reymann
ViroQuant CellNetworks RNAi Screening Facility, BIOQUANT, University of Heidelberg, Germany
Biotechniques 47:877-8. 2009..Here, we present novel 9216-microwell cell arrays which combine the advantages of multiwell plates (physically separated samples) and cell microarrays (high sample density and long-term storage)...
- Transfected cell microarrays: an efficient tool for high-throughput functional analysisVytaute Starkuviene
European Molecular Biology Laboratory, Cell Biology and Cell Biophysics Unit, Heidelberg, Germany
Expert Rev Proteomics 4:479-89. 2007..These advances, combined with an increasing number and diversity of gene perturbing systems, such as RNAi and ectopic gene expression, provide tools for expanding our understanding of biology at the systems level...
- siRNA cell arrays for high-content screening microscopyHolger Erfle
European Molecular Biology Laboratory, Heidelberg, Germany
Biotechniques 37:454-8, 460, 462. 2004..We demonstrate such an siRNA cell array in a microscope-based functional assay in living cells to determine the effect of various siRNA oligonucleotides against endogenous targets on cellular secretion...
- Identification of cholesterol-regulating genes by targeted RNAi screeningFabian Bartz
Institute of Human Genetics, University of Heidelberg, Seminarstrasse 2, Heidelberg, Germany
Cell Metab 10:63-75. 2009..Taken together, TMEM97 and other factors described here are promising to yield further insights into how cells control cholesterol levels...
- The SUMOylation Pathway Restricts Gene Transduction by Adeno-Associated VirusesChristina Hölscher
German Cancer Research Center, Heidelberg, Germany
PLoS Pathog 11:e1005281. 2015..We suggest that transiently targeting SUMOylation will enhance application of AAV in vitro and in vivo. ..
- Robust RNAi enhancement via human Argonaute-2 overexpression from plasmids, viral vectors and cell linesKathleen Börner
Department of Infectious Diseases, Virology, Heidelberg University Hospital, Im Neuenheimer Feld 324, D 69120 Heidelberg, Germany, Cluster of Excellence CellNetworks, Heidelberg University, Im Neuenheimer Feld 267, D 69120 Heidelberg, Germany, Department of Medicine III, University Hospital Aachen, Pauwelstrasse 30, D 52074 Aachen, Germany, Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, D 69120 Heidelberg, Germany, Division Signaling and Functional Genomics, German Cancer Research Center, Im Neuenheimer Feld 580, D 69120 Heidelberg, Germany, BIOQUANT, Heidelberg University, Im Neuenheimer Feld 267, D 69120 Heidelberg, Germany and Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Im Neuenheimer Feld 350, D 69120 Heidelberg, Germany
Nucleic Acids Res 41:e199. 2013..Our customizable reagents and avenues should broadly improve future in vitro and in vivo RNAi experiments in mammalian systems. ..
- Correlative light microscopy for high-content screeningBenjamin Flottmann
BioQuant Centre, Heidelberg University, Heidelberg, Germany
Biotechniques 55:243-52. 2013..As a case study, we visualized and quantified cis- and trans-Golgi markers at increasing resolution...
- An RNAi screen identifies KIF15 as a novel regulator of the endocytic trafficking of integrinAnastasia Eskova
BIOQUANT, University of Heidelberg, 69120 Heidelberg, Germany
J Cell Sci 127:2433-47. 2014..Our data suggest a novel role for KIF15 in mediating plasma membrane localization of the alternative clathrin adaptor Dab2, thus impinging on pathways that regulate α2 integrin internalization. ..
- Production of siRNA- and cDNA-transfected cell arrays on noncoated chambered coverglass for high-content screening microscopy in living cellsHolger Erfle
Cell Biology and Cell Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
Methods Mol Biol 360:155-61. 2007..This method should facilitate drug target validation by small-interfering RNAs...
- Fluorescence microscopy-based RNA interference screeningManuel Gunkel
BIOQUANT, ViroQuant CellNetworks RNAi Screening Facility, Ruprecht Karls Universitat Heidelberg, Im Neuenheimer Feld 267, Heidelberg, 69120, Germany
Methods Mol Biol 1251:59-66. 2015..Additionally, different microscope types for screening approaches are compared and considerations about the information workflow are made...
- Integrated and correlative high-throughput and super-resolution microscopyManuel Gunkel
BioQuant Centre, Heidelberg University, INF 267, 69120, Heidelberg, Germany
Histochem Cell Biol 141:597-603. 2014..This procedure is suitable to combine any kind of fluorescence microscopy technique, in order to gain further insights on the observed specimen at multiple temporal or special scales. ..
- A three-dimensional colocalization RNA interference screening platform to elucidate the alternative lengthening of telomeres pathwaySarah Osterwald
Research Group Genome Organization and Function, DKFZ and BioQuant, Heidelberg, Germany
Biotechnol J 7:103-16. 2012..It extends the available repertoire of high-content screening to studies of cellular colocalizations and allows the identification of candidate genes for the ALT mechanism that represent possible targets for cancer therapy...
- Single-cell-based image analysis of high-throughput cell array screens for quantification of viral infectionPetr Matula
University of Heidelberg, Department of Bioinformatics and Functional Genomics, BIOQUANT, IPMB, Heidelberg, Germany
Cytometry A 75:309-18. 2009..Our image analysis approach allows for the automatic and accurate determination of changes in viral infection based on high-throughput single-cell-based siRNA cell array imaging experiments...
- Identification of HNRNPK as regulator of hepatitis C virus particle productionMarion Poenisch
Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
PLoS Pathog 11:e1004573. 2015..This study adds a new function to HNRNPK that acts as central hub in the replication cycle of multiple other viruses. ..
- The microtubule affinity regulating kinase MARK4 promotes axoneme extension during early ciliogenesisStefanie Kuhns
Molecular Biology of Centrosomes and Cilia group, Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, German Cancer Research Center DKFZ, 69120 Heidelberg, Germany
J Cell Biol 200:505-22. 2013..We propose that MARK4 is a critical positive regulator of early steps in ciliogenesis...
- Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartmentSimon Reiss
The Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany
Cell Host Microbe 9:32-45. 2011..Our analysis suggests that the direct activation of a lipid kinase by HCV NS5A contributes critically to the integrity of the membranous viral replication complex...
- From experimental setup to bioinformatics: an RNAi screening platform to identify host factors involved in HIV-1 replicationKathleen Börner
Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
Biotechnol J 5:39-49. 2010..The ViroQuant-CellNetworks RNAi Screening core facility is an integral part of the recently founded BioQuant centre for systems biology at the University of Heidelberg and will provide service to external users in the near future...
- An RNAi screening platform to identify secretion machinery in mammalian cellsJeremy C Simpson
Cell Biology and Biophysics Unit, European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
J Biotechnol 129:352-65. 2007..Correlating these findings with other screens and bioinformatic information makes these candidates highly likely to be novel membrane traffic machinery components...
- High-throughput RNAi screening by time-lapse imaging of live human cellsBeate Neumann
MitoCheck Project Group, European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
Nat Methods 3:385-90. 2006..This modular platform is scalable and makes the power of time-lapse microscopy available for genome-wide RNAi screens...
- Automatic identification of subcellular phenotypes on human cell arraysChristian Conrad
Intelligent Bioinformatics Systems, German Cancer Research Center DKFZ, 69120 Heidelberg, Germany
Genome Res 14:1130-6. 2004..Our classification method can be adapted to virtually any microscopic assay based on cell morphology, opening a wide range of applications including large-scale RNAi screening in human cells...
- A microscope-based screening platform for large-scale functional protein analysis in intact cellsUrban Liebel
Cell Biology and Cell Biophysics Programme, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
FEBS Lett 554:394-8. 2003..Two automated functional assays addressing protein secretion and the integrity of the Golgi complex were developed and tested. This shows the potential of the system in large-scale, cell-based functional proteomic projects...
- High throughput screening of gene functions in mammalian cells using reversely transfected cell arrays: review and protocolMichael Sturzl
Division of Molecular and Experimental Surgery, Department of Surgery, University of Erlangen Nuremberg, Schwabachanlage 10, D 91054 Erlangen, Germany
Comb Chem High Throughput Screen 11:159-72. 2008..Several different cell types have been successfully used for this procedure. This review summarizes the presently available knowledge on this technique and provides a laboratory protocol...
- High-content screening microscopy identifies novel proteins with a putative role in secretory membrane trafficVytaute Starkuviene
Cell Biology and Biophysics Programme, European Molecular Biology Laboratory EMBL, 69117 Heidelberg, Germany
Genome Res 14:1948-56. 2004..It will also serve as an example for similar microscope-based screens addressing different biological questions...