TY - JOUR
T1 - RNA isolation for transcriptomics of human and mouse small skin biopsies
AU - Bruning, Oskar
AU - Rodenburg, Wendy
AU - Radonic, Teodora
AU - Zwinderman, Aeilko H.
AU - De Vries, Annemieke
AU - Breit, Timo M.
AU - De Jong, Mark
N1 - Funding Information: This work was partly supported by NIEHS 72-SNP grant 1R01 ES015587-01A2 and by the Interuniversity Cardiology Institute of the Netherlands (ICIN) and Dutch Marfan Association. The study is partly funded by the Dutch Heart Association, grant 2008B115.
PY - 2011
Y1 - 2011
N2 - Background: 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. Findings. 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 g with an average RNA quality RIN value of 8.1. For the mouse biopsies, the average RNA yield was 2.4 g 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. Conclusions: 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.
AB - Background: 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. Findings. 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 g with an average RNA quality RIN value of 8.1. For the mouse biopsies, the average RNA yield was 2.4 g 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. Conclusions: 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.
UR - http://www.scopus.com/inward/record.url?scp=80054818771&partnerID=8YFLogxK
U2 - https://doi.org/10.1186/1756-0500-4-438
DO - https://doi.org/10.1186/1756-0500-4-438
M3 - Article
C2 - 22023775
SN - 1756-0500
VL - 4
SP - 438
JO - BMC Research Notes
JF - BMC Research Notes
IS - 1
M1 - 438
ER -