Datasets assessing lipid-content in optically cleared brains

Shimrit Oz; Galit Saar; Shunit Olszakier; Ronit Heinrich; Mykhail O Kompanets; Shai Berlin

doi:10.1016/j.dib.2023.109795

Datasets assessing lipid-content in optically cleared brains

Data Brief. 2023 Nov 30:52:109795. doi: 10.1016/j.dib.2023.109795. eCollection 2024 Feb.

Authors

Shimrit Oz¹, Galit Saar², Shunit Olszakier¹, Ronit Heinrich¹, Mykhail O Kompanets³, Shai Berlin¹

Affiliations

¹ Department of Neuroscience, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel.
² Biomedical Core Facility, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel.
³ L.M. Litvinenko Institute of Physico-Organic Chemistry and Coal Chemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine.

Abstract

Multi-modal imaging, by light-microscopy (LM) and Magnetic Resonance Imaging (MRI), holds promise for examining the brain across various resolutions and scales. While MRI acquires images in three dimensions, acquisition of intact whole-brain by LM requires a process of tissue clearing that renders the brain transparent. Removal of lipids (delipidation) is a critical step in the tissue clearing process, and was previsouly suggested to be the cause for absence of MRI contrast in cleared brains. Yet, the association between MRI contrast, delipidation and the different clearing techniques is debatable. Here, we provide datasets concerning lipid-content in cleared brain tissues obtained by various approaches. Fixed mouse and rat brains were cleared by CLARITY, Scale, uDISCO and ECi clearing techniques. Lipid-content was assessed at various intermediate steps of the different clearing methods, as well as at the end of the processes. Methods employed included whole brain MRI acquisition, Oil Red O (ORO)- and carbocyanine DiI-staining of cryosections, and DiI-washout assay from brain slices. MRI contrast-to-noise ratio, staining intensities and integrity of tissue were systematically analyzed. We demonstrate that lipid electrophoresis, an essential step of the CLARITY approach, engenders progressive reduction in MRI contrast in non-cleared (PFA-fixed) control brains, as well as strongly reduces contrast from uDISCO and ECi-cleared brains. ORO minimally stained CLARITY-cleared brains, however efficiently labelled uDISCO and ECi-cleared brains. Conversely, and in contrast to ORO-staining, DiI equally stained control, CLARITY, ECi and uDISCO-cleared brains. Both ORO- and DiI-staining demonstrated impairment in brain tissue integrity following CLARITY, but less so in uDISCO and ECi brains. DiI-washout assay demonstrated that each of the solvents employed along the process of uDISCO and ECi are highly delipidating, as well as the SDS-electrophoresis employed during CLARITY clearing. However, Scale treatment preserved most of the DiI dye. These data emphasize the variability in lipid assessment of cleared tissues by common techniques, and may help to resolve the contribution of lipids in brain MRI contrast.

Keywords: Fluorescent probe; Histochemistry; Imaging; Lipids; MRI; Tissue-clearing.