Methods
Imaging of telomere features
Contact: M. Gunkel, H. Erfle group and I. Chung, K. Deeg, in the K. Rippe group
- Automated targeted 3D imaging using a combined widefield and confocal laser scanning microscopy
- Super-resolution microscopy (PALM, STORM)
- FISH and immunostaining
- Fluorescence microscopy based visualization of ALT-asscociated PML bodies, protocol for stainig
- Chromosome orientation FISH (CO-FISH) , protocol for staining
- TERRA RNA-FISH
more information about the imaging methodes can be found in
- Osterwald, S. et al. A three-dimensional colocalization RNA interference screening platform to elucidate the alternative lengthening of telomeres pathway. (2012) Biotechnol J 7, 103-116 doi: 10.1002/biot.201000474
- Wörtz, S. et al. 3D geometry-based quantification of colocalizations in multichannel 3D microscopy images of human soft tissue tumors. (2010) IEEE Transactions on Medical Imaging 29, 1474-1484 doi: 10.1109/TMI.2010.2049857
- Gunkel M. et al. (2016). Quantification of telomere features in tumor tissue sections by an automated 3D imaging-based workflow. bioRxiv doi: 10.1101/053132 | Abstract | Preprint (4.4 MB).
Experimental methods to dissect telomere maintenance mechansims
Contact: I. Chung, K. Deeg, in the K. Rippe group & Brian Luke
- Terminal restriction fragment (TRF) heterogeneity analysis, protocol
- C-circle assay, protocol
- Telomere-repeat quantitative PCR, protocol
- Reverse transcription quantitative PCR of TERRA, protocol
- TERRA RNA dot blot
Bioinformatical analysis and modeling
Image analysis methods
Contact: S. Wörz, K. Rohr group
- 3D segmentation of subcellular structures (e.g., telomeres) in 3D microscopy images of cell lines and tissue microarrays (TMAs)
- Determination of 3D colocalization (e.g., telomeres and PML bodies)
- Quantification of cytological features (e.g.., telomere length distribution)
Modeling of telomere maintenance mechanisms
Contact: A. Poos, R. König group
- MIPRIP: The Mixed Integer linear Programming based Regulatory Interaction Predictor (R-package, publication)
Analysis of telomere features from deep sequencing data
Contact: L. Feuerbach
- TelomereHunter: Telomere length analysis from genome sequencing data (Python script)
Telomere maintenance genes
Contact: D. Braun, N. Kepper in the K. Rippe group
- TelNet database of human and yeast genes that are involved in telomere maintenance, see TelNet web page.
ALT prediction in tumors
Contact: I. Chung in the K. Rippe group, and A. Poos in the R. König group
- PAINT is a classification scheme for predicting the active telomere maintenance mechanism, see PAINT web page.
