Near-isotropic, reconstructed volume electron microscopy (FIB-SEM) of mouse kidney (jrc_mus-kidney-2)
Sample: Wild-type, 8 week old mouse, strain: C57BL/6 from Jackson Lab
Sample Description: This dataset features isotropic 3D electron microscopy data of the mouse kidney (jrc_mus-kidney-2). The sample was obtained from an 8-week-old wild-type C57BL/6 mouse strain, sourced from Jackson Laboratory. Euthanasia was performed in accordance with IACUC guidelines, with perfusion conducted by Shu-Hsien.
The sample preparation involved cutting 1.5 mm punches from 100 µm-thick vibratome slices. High-pressure freezing (HPF) was performed using the Wohlwend HPF. Freeze substitution (FS) was carried out with 0.5% OsO₄, 0.1% uranyl acetate, and 20 mM 1,2,4 triazole in acetone, followed by acetone rinses. The sample was infiltrated with increasing concentrations of Durcupan in acetone, followed by three exchanges with 100% Durcupan. The embedding was completed in 100% Durcupan and cured at 60°C for 48 hours.
Shu-Hsien Shu was responsible for the perfusion, while Nirmala Iyer (HHMI/Janelia) handled HPF, freeze substitution, and resin embedding. Zhiyuan Lu (HHMI/Janelia) trimmed the sample for FIBSEM, and Wei Qiu (HHMI/Janelia) performed the imaging. Post-processing was completed by Eric Trautman and Stephan Preibisch (HHMI/Janelia).
This dataset offers a detailed view of the cellular architecture of a young mouse kidney, providing valuable data for research in nephrology and related fields.
Protocol: Mouse euthanasia was performed as IACUC guidelines. Perfusion by Shu-Hsien.1.5 mm punches were cut out of 100µm thick vibratome slices and HPF using the Wohlwend HPF. FS using 0.5% OsO4, 0.1% UA,20mM 1,2,4 triazole in acetone. Acetone rinses followed by infiltration with increasing concentrations of Durcupan in Acetone and 3 exchanges of 100% Durcupan. Embedding in 100% Durcupan and curing at 60 degrees for 48 hours.
Contributions: Sample preparation by Shu-Hsien Shu (perfusion) and Nirmala Iyer (HHMI/ Janelia) - HPF FS and resin embedding. Trimmed for FIBSEM by Zhiyuan Lu (HHMI/Janelia), and imaged by Wei Qiu (HHMI/Janelia) and post-processing by Eric Trautman and Stephan Preibisch (HHMI/Janelia).
Acquisition ID: jrc_mus-kidney-2
Voxel size (nm): 8.0 x 8.0 x 8.0 (X, Y, Z)
Imaging duration (days): 13
Data dimensions (µm): 102.992 x 101.464 x 110.536 (X,Y,Z)
Imaging start date: 2022-11-01
Dataset URL (Redirect): https://data.janelia.org/X0Ata
Visualization Website: https://openorganelle.janelia.org/datasets/jrc_mus-kidney-2
