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RNA isolation for transcriptomics of human and mouse small skin biopsies

Oskar Bruning1, Wendy Rodenburg2, Teodora Radonic3, Aeilko H Zwinderman3, Annemieke de Vries2, Timo M Breit1* and Mark de Jong1

Author Affiliations

1 MicroArray Department & Integrative Bioinformatics Unit (MAD-IBU), Swammerdam Institute for Life Sciences (SILS); Faculty of Science (FNWI), University of Amsterdam (UvA), Science Park 904, 1098 XH Amsterdam, The Netherlands

2 Laboratory for Health Protection Research (GBO), National Institute of Public Health and the Environment (RIVM), Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, The Netherlands

3 Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center (AMC) Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands

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BMC Research Notes 2011, 4:438  doi:10.1186/1756-0500-4-438

Published: 24 October 2011



Isolation of RNA from skin biopsies presents a challenge, due to the tough nature of skin tissue and a high presence of RNases. As we lacked the dedicated equipment, i.e. homogenizer or bead-beater, needed for the available RNA from skin isolation methods, we adapted and tested our zebrafish single-embryo RNA-isolation protocol for RNA isolation from skin punch biopsies.


We tested our new RNA-isolation protocol in two experiments: a large-scale study with 97 human skin samples, and a small study with 16 mouse skin samples. Human skin was sampled with 4.0 mm biopsy punches and for the mouse skin different punch diameter sizes were tested; 1.0, 1.5, 2.0, and 2.5 mm. The average RNA yield in human samples was 1.5 μg with an average RNA quality RIN value of 8.1. For the mouse biopsies, the average RNA yield was 2.4 μg with an average RIN value of 7.5. For 96% of the human biopsies and 100% of the mouse biopsies we obtained enough high-quality RNA. The RNA samples were successfully tested in a transcriptomics analysis using the Affymetrix and Roche NimbleGen platforms.


Using our new RNA-isolation protocol, we were able to consistently isolate high-quality RNA, which is apt for further transcriptomics analysis. Furthermore, this method is already useable on biopsy material obtained with a punch diameter as small as 1.5 mm.