Center for Molecular Medicine Cologne

Gene Expression Affymetrix Facility

Gene Expression Affymetrix Facility at the CMMC is headed by Prof. Dr. Agapios Sachinidis (Institute for Neurophysiology) and his team, Dipl. Biol. Margit Henry and Dipl. Biol. Tamara Rotshteyn.


Besides 3’ transcriptomics microarrays, the Facility also uses the GeneChip® Human Transcriptome Array 2.0, the GeneChip® Mouse Exon ST Array and the GeneChip® Rat Exon ST Array. These arrays offer a cost-effective alternative to next generation sequencing with the following main advantages:

  • Analysis of the data does not require specific knowledge in bioinformatics
  • Big data storage facilities are not required
  • Analysis of the data is very fast

Before sending samples, please get in contact with Margit Henry or Tamara Rotshteyn.


Postal address for sending the samples:
Gene Expression Affymetrix Facility
CMMC Research Building
Robert-Koch-Str. 21
50931 Cologne

 

Please note that the Facility cannot guarantee a positive outcome and that remaining samples can only be stored for 4 weeks, after which they will be discarded.

 

Acharya, A., Brungs, S., Lichterfeld, Y., Hescheler, J., Hemmersbach, R., Boeuf, H., and Sachinidis, A. (2019). Parabolic, Flight-Induced, Acute Hypergravity and Microgravity Effects on the Beating Rate of Human Cardiomyocytes. Cells 8.

Ahuja, G., Bartsch, D., Yao, W., Geissen, S., Frank, S., Aguirre, A., Russ, N., Messling, J.E., Dodzian, J., Lagerborg, K.A., Vargas, N.E., Muck, J.S., Brodesser, S., Baldus, S., Sachinidis, A., Hescheler, J., Dieterich, C., Trifunovic, A., Papantonis, A., Petrascheck, M., Klinke, A., Jain, M., Valenzano, D.R., and Kurian, L. (2019). Loss of genomic integrity induced by lysosphingolipid imbalance drives ageing in the heart. EMBO Rep 20.

Albrecht, W., Kappenberg, F., Brecklinghaus, T., Stoeber, R., Marchan, R., Zhang, M., Ebbert, K., Kirschner, H., Grinberg, M., Leist, M., Moritz, W., Cadenas, C., Ghallab, A., Reinders, J., Vartak, N., van Thriel, C., Golka, K., Tolosa, L., Castell, J.V., Damm, G., Seehofer, D., Lampen, A., Braeuning, A., Buhrke, T., Behr, A.C., Oberemm, A., Gu, X., Kittana, N., van de Water, B., Kreiling, R., Fayyaz, S., van Aerts, L., Smedsrod, B., Ellinger-Ziegelbauer, H., Steger-Hartmann, T., Gundert-Remy, U., Zeigerer, A., Ullrich, A., Runge, D., Lee, S.M.L., Schiergens, T.S., Kuepfer, L., Aguayo-Orozco, A., Sachinidis, A., Edlund, K., Gardner, I., Rahnenfuhrer, J., and Hengstler, J.G. (2019). Prediction of human drug-induced liver injury (DILI) in relation to oral doses and blood concentrations. Arch Toxicol 93, 1609-37.

Argenziano, M.A., Doss, M.X., Tabler, M., Sachinidis, A., and Antzelevitch, C. (2019). Transcriptional changes associated with advancing stages of heart failure underlie atrial and ventricular arrhythmogenesis. PLoS One 14, e0216928.

Frank, S., Ahuja, G., Bartsch, D., Russ, N., Yao, W., Kuo, J.C., Derks, J.P., Akhade, V.S., Kargapolova, Y., Georgomanolis, T., Messling, J.E., Gramm, M., Brant, L., Rehimi, R., Vargas, N.E., Kuroczik, A., Yang, T.P., Sahito, R.G.A., Franzen, J., Hescheler, J., Sachinidis, A., Peifer, M., Rada-Iglesias, A., Kanduri, M., Costa, I.G., Kanduri, C., Papantonis, A., and Kurian, L. (2019). yylncT Defines a Class of Divergently Transcribed lncRNAs and Safeguards the T-mediated Mesodermal Commitment of Human PSCs. Cell Stem Cell 24, 318-27 e8.

Sachinidis, A., Albrecht, W., Nell, P., Cherianidou, A., Hewitt, N.J., Edlund, K., and Hengstler, J.G. (2019). Road Map for Development of Stem Cell-Based Alternative Test Methods. Trends Mol Med 25, 470-81.

Santos, J.M.A., Mendes-Silva, L., Afonso, V., Martins, G., Machado, R.S.R., Lopes, J.A., Cancela, L., Futschik, M.E., Sachinidis, A., Gavaia, P., and Braganca, J. (2019). Exogenous WNT5A and WNT11 proteins rescue CITED2 dysfunction in mouse embryonic stem cells and zebrafish morphants. Cell Death Dis 10, 582.

Acharya, A., Brungs, S., Henry, M., Rotshteyn, T., Singh Yaduvanshi, N., Wegener, L., Jentzsch, S., Hescheler, J., Hemmersbach, R., Boeuf, H., and Sachinidis, A. (2018). Modulation of Differentiation Processes in Murine Embryonic Stem Cells Exposed to Parabolic Flight-Induced Acute Hypergravity and Microgravity. Stem Cells Dev 27, 838-47.

Chaudhari, U., Nemade, H., Sureshkumar, P., Vinken, M., Ates, G., Rogiers, V., Hescheler, J., Hengstler, J.G., and Sachinidis, A. (2018). Functional cardiotoxicity assessment of cosmetic compounds using human-induced pluripotent stem cell-derived cardiomyocytes. Arch Toxicol 92, 371-81.

Filipova, D., Henry, M., Rotshteyn, T., Brunn, A., Carstov, M., Deckert, M., Hescheler, J., Sachinidis, A., Pfitzer, G., and Papadopoulos, S. (2018). Distinct transcriptomic changes in E14.5 mouse skeletal muscle lacking RYR1 or Cav1.1 converge at E18.5. PLoS One 13, e0194428.

Grinberg, M., Stober, R.M., Albrecht, W., Edlund, K., Schug, M., Godoy, P., Cadenas, C., Marchan, R., Lampen, A., Braeuning, A., Buhrke, T., Leist, M., Oberemm, A., Hellwig, B., Kamp, H., Gardner, I., Escher, S., Taboureau, O., Aguayo-Orozco, A., Sachinidis, A., Ellinger-Ziegelbauer, H., Rahnenfuhrer, J., and Hengstler, J.G. (2018). Toxicogenomics directory of rat hepatotoxicants in vivo and in cultivated hepatocytes. Arch Toxicol 92, 3517-33.

Limonciel, A., van Breda, S.G., Jiang, X., Tredwell, G.D., Wilmes, A., Aschauer, L., Siskos, A.P., Sachinidis, A., Keun, H.C., Kopp-Schneider, A., de Kok, T.M., Kleinjans, J.C.S., and Jennings, P. (2018). Persistence of Epigenomic Effects After Recovery From Repeated Treatment With Two Nephrocarcinogens. Front Genet 9, 558.

Nemade, H., Chaudhari, U., Acharya, A., Hescheler, J., Hengstler, J.G., Papadopoulos, S., and Sachinidis, A. (2018). Cell death mechanisms of the anti-cancer drug etoposide on human cardiomyocytes isolated from pluripotent stem cells. Arch Toxicol 92, 1507-24.

Rodrigues, R.M., Kollipara, L., Chaudhari, U., Sachinidis, A., Zahedi, R.P., Sickmann, A., Kopp-Schneider, A., Jiang, X., Keun, H., Hengstler, J., Oorts, M., Annaert, P., Hoeben, E., Gijbels, E., De Kock, J., Vanhaecke, T., Rogiers, V., and Vinken, M. (2018). Omics-based responses induced by bosentan in human hepatoma HepaRG cell cultures. Arch Toxicol 92, 1939-52.

Sabour, D., Machado, R.S.R., Pinto, J.P., Rohani, S., Sahito, R.G.A., Hescheler, J., Futschik, M.E., and Sachinidis, A. (2018). Parallel Genome-wide Profiling of Coding and Non-coding RNAs to Identify Novel Regulatory Elements in Embryonic and Maturated Heart. Mol Ther Nucleic Acids 12, 158-73.

Chaudhari, U., Ellis, J.K., Wagh, V., Nemade, H., Hescheler, J., Keun, H.C., and Sachinidis, A. (2017). Metabolite signatures of doxorubicin induced toxicity in human induced pluripotent stem cell-derived cardiomyocytes. Amino Acids 49, 1955-63.

Chaudhari, U., Nemade, H., Sureshkumar, P., Vinken, M., Ates, G., Rogiers, V., Hescheler, J., Hengstler, J.G., and Sachinidis, A. (2018). Functional cardiotoxicity assessment of cosmetic compounds using human-induced pluripotent stem cell-derived cardiomyocytes. Arch Toxicol 92, 371-81.

Colaianna, M., Ilmjarv, S., Peterson, H., Kern, I., Julien, S., Baquie, M., Pallocca, G., Bosgra, S., Sachinidis, A., Hengstler, J.G., Leist, M., and Krause, K.H. (2017). Fingerprinting of neurotoxic compounds using a mouse embryonic stem cell dual luminescence reporter assay. Arch Toxicol 91, 365-91.

Gaspar, J.A., Srinivasan, S.P., Sureshkumar, P., Doss, M.X., Hescheler, J., Papadopoulos, S., and Sachinidis, A. (2017). Depletion of Mageb16 induces differentiation of pluripotent stem cells predominantly into mesodermal derivatives. Sci Rep 7, 14285.

Sabour, D., Srinivasan, S.P., Rohani, S., Wagh, V., Gaspar, J.A., Panek, D., Ardestani, M.A., Doss, M.X., Riet, N., Abken, H., Hescheler, J., Papadopoulos, S., and Sachinidis, A. (2017). STRIP2 Is Indispensable for the Onset of Embryonic Stem Cell Differentiation. Mol Ther Methods Clin Dev 5, 116-29.

Shinde, V., Hoelting, L., Srinivasan, S.P., Meisig, J., Meganathan, K., Jagtap, S., Grinberg, M., Liebing, J., Bluethgen, N., Rahnenfuhrer, J., Rempel, E., Stoeber, R., Schildknecht, S., Forster, S., Godoy, P., van Thriel, C., Gaspar, J.A., Hescheler, J., Waldmann, T., Hengstler, J.G., Leist, M., and Sachinidis, A. (2017). Definition of transcriptome-based indices for quantitative characterization of chemically disturbed stem cell development: introduction of the STOP-Toxukn and STOP-Toxukk tests. Arch Toxicol 91, 839-64.

Head

Prof. Dr. Agapios Sachinidis CMMC Cologne
Prof. Dr. Agapios Sachinidis

Institute for Neurophysiology / RG location - CMMC Building

Head - Affymetrix Facility

+ 49 221 478 7373

+ 49 221 478 3984

Institute for Neurophysiology / RG location - CMMC Building

http://physiologie.uni-koeln.de/560.html

CMMC Profile Page

Data analysis support

Contact

Dipl. Biol. Margit Henry CMMC Cologne
Dipl. Biol. Margit Henry

Gene Expression Affymetrix Facility

+ 49 221 478 89794

+49 221 478 78910

Gene Expression Affymetrix Facility

Robert-Koch-Str. 21

50931 Cologne

CMMC Profile Page

Dipl. Biol. Tamara Rotshteyn CMMC Cologne
Dipl. Biol. Tamara Rotshteyn

Gene Expression Affymetrix Facility

+ 49 221 478 89794

+49 221 478 78910

Gene Expression Affymetrix Facility

Robert-Koch-Str. 21

50931 Cologne

CMMC Profile Page

Location

Gene Expression Affymetrix Facility
CMMC Research Building
2nd floor (room 2.018 and 2.019)
Robert-Koch-Str. 21
50931 Cologne.