Protocol for tissue clearing and 3D analysis of dopamine neurons in the developing mouse midbrain

Youri Adolfs; Divya D.A. Raj; Sara Brignani; R. Jeroen Pasterkamp

doi:10.1016/j.xpro.2021.100669

Protocol for tissue clearing and 3D analysis of dopamine neurons in the developing mouse midbrain

Youri Adolfs, Divya D.A. Raj, Sara Brignani, R. Jeroen Pasterkamp^*

^*Corresponding author for this work

Neurology

Research output: Contribution to journal › Article › peer-review

4 Scopus citations

Abstract

Advances in tissue clearing enable analysis of complex migratory patterns of developing neurons in whole intact tissue. Here, we implemented a modified version of 3DISCO to study migration of midbrain dopamine (DA) neurons. We provide a detailed protocol starting from whole-brain immunostaining, tissue clearing, and ultramicroscopic imaging to post-acquisition quantification and analysis. This protocol enables precise quantification of DA neuron migration but can also be applied more generally for analyzing neuron migration throughout the nervous system. For complete details on the use and execution of this protocol, please refer to Brignani et al. (2020).

Original language	English (US)
Article number	100669
Journal	STAR Protocols
Volume	2
Issue number	3
DOIs	https://doi.org/10.1016/j.xpro.2021.100669
State	Published - Sep 17 2021

Funding

We thank Dr. Alain Chedotal for training provided to Y.A. We thank Dr. Eljo Y van Battum for help in setting up the 3DISCO protocol at the MIND facility (mindresearchfacility.nl). We thank Roger Koot for IT support. This work was supported by mDANeurodev, FP/2007\u20132011, Grant 222999; Dutch Top Institute Pharma Project T5-207; Universiteit Utrecht (MIND research facility, Dynamics of Youth); the People Program (Marie Curie Actions) of the European Union's Seventh Framework Program (FP7) 2007\u20132013 under REA grant agreement number 289581 (NPlast); Netherlands Organization for Scientific Research (ALW-NWO VICI); and Stichting Parkinson Fonds to R.J.P. R.J.P. is funded through the Gravitation program of the Dutch Ministry of Education, Culture, and Science and the Netherlands Organization for Scientific Research. Y.A. D.D.A.R. S.B. and R.J.P. conceived the project; Y.A. set up ultramicroscopy imaging in the MIND facility (MIND research facility; www.mindresearchfacility.nl); Y.A. with help of the other authors, optimized and conducted immunostaining and imaging; Y.A. conceived the quantitative method for Imaris\u2122 analysis with help from D.D.A.R. and S.B.; Y.A. and R.J. wrote the manuscript with help from D.D.A.R. and S.B. The authors declare no competing interests. We thank Dr. Alain Chedotal for training provided to Y.A. We thank Dr. Eljo Y van Battum for help in setting up the 3DISCO protocol at the MIND facility (mindresearchfacility.nl). We thank Roger Koot for IT support. This work was supported by mDANeurodev, FP/2007\u20132011, Grant 222999; Dutch Top Institute Pharma Project T5-207 ; Universiteit Utrecht (MIND research facility, Dynamics of Youth); the People Program (Marie Curie Actions) of the European Union\u2019s Seventh Framework Program (FP7) 2007\u20132013 under REA grant agreement number 289581 (NPlast); Netherlands Organization for Scientific Research (ALW-NWO VICI); and Stichting Parkinson Fonds to R.J.P. R.J.P. is funded through the Gravitation program of the Dutch Ministry of Education, Culture, and Science and the Netherlands Organization for Scientific Research .

Keywords

Antibody
Microscopy
Model Organisms
Molecular Biology
Neuroscience

ASJC Scopus subject areas

General Biochemistry, Genetics and Molecular Biology
General Neuroscience
General Immunology and Microbiology
General Medicine

Access to Document

10.1016/j.xpro.2021.100669

Cite this

@article{631cde1e6b9e44bfb0330fca8a475bbf,

title = "Protocol for tissue clearing and 3D analysis of dopamine neurons in the developing mouse midbrain",

abstract = "Advances in tissue clearing enable analysis of complex migratory patterns of developing neurons in whole intact tissue. Here, we implemented a modified version of 3DISCO to study migration of midbrain dopamine (DA) neurons. We provide a detailed protocol starting from whole-brain immunostaining, tissue clearing, and ultramicroscopic imaging to post-acquisition quantification and analysis. This protocol enables precise quantification of DA neuron migration but can also be applied more generally for analyzing neuron migration throughout the nervous system. For complete details on the use and execution of this protocol, please refer to Brignani et al. (2020).",

keywords = "Antibody, Microscopy, Model Organisms, Molecular Biology, Neuroscience",

author = "Youri Adolfs and Raj, {Divya D.A.} and Sara Brignani and Pasterkamp, {R. Jeroen}",

note = "Funding Information: We thank Dr. Alain Chedotal for training provided to Y.A. We thank Dr. Eljo Y van Battum for help in setting up the 3DISCO protocol at the MIND facility (mindresearchfacility.nl). We thank Roger Koot for IT support. This work was supported by mDANeurodev, FP/2007–2011, Grant 222999; Dutch Top Institute Pharma Project T5-207; Universiteit Utrecht (MIND research facility, Dynamics of Youth); the People Program (Marie Curie Actions) of the European Union's Seventh Framework Program (FP7) 2007–2013 under REA grant agreement number 289581 (NPlast); Netherlands Organization for Scientific Research (ALW-NWO VICI); and Stichting Parkinson Fonds to R.J.P. R.J.P. is funded through the Gravitation program of the Dutch Ministry of Education, Culture, and Science and the Netherlands Organization for Scientific Research. Y.A. D.D.A.R. S.B. and R.J.P. conceived the project; Y.A. set up ultramicroscopy imaging in the MIND facility (MIND research facility; www.mindresearchfacility.nl); Y.A. with help of the other authors, optimized and conducted immunostaining and imaging; Y.A. conceived the quantitative method for Imaris{\texttrademark} analysis with help from D.D.A.R. and S.B.; Y.A. and R.J. wrote the manuscript with help from D.D.A.R. and S.B. The authors declare no competing interests. Funding Information: We thank Dr. Alain Chedotal for training provided to Y.A. We thank Dr. Eljo Y van Battum for help in setting up the 3DISCO protocol at the MIND facility (mindresearchfacility.nl). We thank Roger Koot for IT support. This work was supported by mDANeurodev, FP/2007–2011, Grant 222999; Dutch Top Institute Pharma Project T5-207 ; Universiteit Utrecht (MIND research facility, Dynamics of Youth); the People Program (Marie Curie Actions) of the European Union{\textquoteright}s Seventh Framework Program (FP7) 2007–2013 under REA grant agreement number 289581 (NPlast); Netherlands Organization for Scientific Research (ALW-NWO VICI); and Stichting Parkinson Fonds to R.J.P. R.J.P. is funded through the Gravitation program of the Dutch Ministry of Education, Culture, and Science and the Netherlands Organization for Scientific Research . Publisher Copyright: {\textcopyright} 2021 The Author(s)",

year = "2021",

month = sep,

day = "17",

doi = "10.1016/j.xpro.2021.100669",

language = "English (US)",

volume = "2",

journal = "STAR Protocols",

issn = "2666-1667",

publisher = "Cell Press",

number = "3",

}

TY - JOUR

T1 - Protocol for tissue clearing and 3D analysis of dopamine neurons in the developing mouse midbrain

AU - Adolfs, Youri

AU - Raj, Divya D.A.

AU - Brignani, Sara

AU - Pasterkamp, R. Jeroen

N1 - Funding Information: We thank Dr. Alain Chedotal for training provided to Y.A. We thank Dr. Eljo Y van Battum for help in setting up the 3DISCO protocol at the MIND facility (mindresearchfacility.nl). We thank Roger Koot for IT support. This work was supported by mDANeurodev, FP/2007–2011, Grant 222999; Dutch Top Institute Pharma Project T5-207; Universiteit Utrecht (MIND research facility, Dynamics of Youth); the People Program (Marie Curie Actions) of the European Union's Seventh Framework Program (FP7) 2007–2013 under REA grant agreement number 289581 (NPlast); Netherlands Organization for Scientific Research (ALW-NWO VICI); and Stichting Parkinson Fonds to R.J.P. R.J.P. is funded through the Gravitation program of the Dutch Ministry of Education, Culture, and Science and the Netherlands Organization for Scientific Research. Y.A. D.D.A.R. S.B. and R.J.P. conceived the project; Y.A. set up ultramicroscopy imaging in the MIND facility (MIND research facility; www.mindresearchfacility.nl); Y.A. with help of the other authors, optimized and conducted immunostaining and imaging; Y.A. conceived the quantitative method for Imaris™ analysis with help from D.D.A.R. and S.B.; Y.A. and R.J. wrote the manuscript with help from D.D.A.R. and S.B. The authors declare no competing interests. Funding Information: We thank Dr. Alain Chedotal for training provided to Y.A. We thank Dr. Eljo Y van Battum for help in setting up the 3DISCO protocol at the MIND facility (mindresearchfacility.nl). We thank Roger Koot for IT support. This work was supported by mDANeurodev, FP/2007–2011, Grant 222999; Dutch Top Institute Pharma Project T5-207 ; Universiteit Utrecht (MIND research facility, Dynamics of Youth); the People Program (Marie Curie Actions) of the European Union’s Seventh Framework Program (FP7) 2007–2013 under REA grant agreement number 289581 (NPlast); Netherlands Organization for Scientific Research (ALW-NWO VICI); and Stichting Parkinson Fonds to R.J.P. R.J.P. is funded through the Gravitation program of the Dutch Ministry of Education, Culture, and Science and the Netherlands Organization for Scientific Research . Publisher Copyright: © 2021 The Author(s)

PY - 2021/9/17

Y1 - 2021/9/17

N2 - Advances in tissue clearing enable analysis of complex migratory patterns of developing neurons in whole intact tissue. Here, we implemented a modified version of 3DISCO to study migration of midbrain dopamine (DA) neurons. We provide a detailed protocol starting from whole-brain immunostaining, tissue clearing, and ultramicroscopic imaging to post-acquisition quantification and analysis. This protocol enables precise quantification of DA neuron migration but can also be applied more generally for analyzing neuron migration throughout the nervous system. For complete details on the use and execution of this protocol, please refer to Brignani et al. (2020).

AB - Advances in tissue clearing enable analysis of complex migratory patterns of developing neurons in whole intact tissue. Here, we implemented a modified version of 3DISCO to study migration of midbrain dopamine (DA) neurons. We provide a detailed protocol starting from whole-brain immunostaining, tissue clearing, and ultramicroscopic imaging to post-acquisition quantification and analysis. This protocol enables precise quantification of DA neuron migration but can also be applied more generally for analyzing neuron migration throughout the nervous system. For complete details on the use and execution of this protocol, please refer to Brignani et al. (2020).

KW - Antibody

KW - Microscopy

KW - Model Organisms

KW - Molecular Biology

KW - Neuroscience

UR - http://www.scopus.com/inward/record.url?scp=85111800043&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85111800043&partnerID=8YFLogxK

U2 - 10.1016/j.xpro.2021.100669

DO - 10.1016/j.xpro.2021.100669

M3 - Article

C2 - 34377993

AN - SCOPUS:85111800043

SN - 2666-1667

VL - 2

JO - STAR Protocols

JF - STAR Protocols

IS - 3

M1 - 100669

ER -

Protocol for tissue clearing and 3D analysis of dopamine neurons in the developing mouse midbrain

Abstract

Funding

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this