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Each step of this microdissection of a wild type endolymphatic sac from a postnatal day 5 (P5) mouse is detailed in the associated video and snapshots of the key steps of this dissection and opening of the endolymphatic sac are presented in Figure 1 and Figure 2.
Representative results of the dissections of the endolymphatic sac with tdTomato fluorescence at embryonic day 16.5 (E16.5), P5 and P30, following this protocol are presented in Figure 3 and in Supplementary Figure 1 and Supplementary Figure 2. Using a dissection microscope with fluorescence, the endolymphatic sac can be readily visualized in the skull after removal of the brain in mice carrying the transgene Tg(ATP6V1B1-Cre) in the presence of the reporter of Cre expression: Ai9 (LSL-RCL-tdT) (see Figure 3A-B, and Supplementary Figure 1 for images captured in incident light and tdTomato fluorescence of the endolymphatic sac at different stages of the dissection). In these mice, Cre is expressed as a mosaic in cells all along the endolymphatic sac and duct (Figure 3, see also Supplementary Figure 2 for visualization of the endolymphatic sac with versus without fluorescent reporter). Although the expression of this reporter is not specific for the endogenous expression of Atp6v1b1, which is restricted to the mitochondria-rich cells of the endolymphatic sac16, one of the two cell types of this epithelium (Figure 5E), it is a helpful aid to identify and dissect the endolymphatic sac.
Inner ears dissected from a mouse model for enlargement of the vestibular aqueduct are presented in Figure 4. As compared to control littermates, the endolymphatic sacs and ducts of mice deficient for SLC26A4 (pendrin) are enlarged.
Representative images of immunohistochemistry of intact endolymphatic sac with and without conjunctive tissue are shown in Figure 5. Results of immunohistochemistry of opened endolymphatic sac of a P5 wild type mouse are also presented (Figure 5F-G). The endolymphatic sac is composed of a single layer of epithelium folded in a pouch-shaped structure, containing in its lumen endolymph. This epithelium consists of two cell types, mitochondria-rich cells and ribosome-rich cells (Figure 5E). A whole-mount endolymphatic sac will be flattened because endolymph is no longer present. The sac will appear as two intertwined layers of epithelium, making it difficult to determine subcellular localization of proteins expressed in this epithelium. By opening the endolymphatic sac, the single layer epithelium can be readily visualized and the relative distribution of the proteins of interest, with respect to the endolymphatic sac lumen, can be determined more definitively. A potential apical (luminal, where endolymph would be) versus basal enrichment of these proteins can be more accurately determined. As an example, SLC26A4 is enriched on the apical side of mitochondria-rich cells (Figure 5F).

Figure 1. Whole-mount dissection of the endolymphatic sac of a wild type mouse at post natal day 5 (P5).
(A) Schematic of the membranous labyrinth of a developed mouse inner ear (right). The location of the endolymphatic sac, and the cochlea and vestibular structures are indicated. This figure has been modified from Honda et al.16.
(B) Mid-sagittal section showing the left hemi-skull. The location of the endolymphatic sac is indicated (arrow). (O, occipital; F, frontal)
(C) Otic capsule along with the squamous part of the temporal bone.
(D) Important landmarks overlaid onto the dotted box in panel C. (ES, endolymphatic sac; ED, endolymphatic duct; VA, vestibular aqueduct; ASC, anterior semicircular canal; PSC, posterior semicircular canal; CC, common crus; SS, sigmoid sinus)
(E) Schematic illustration of the cross-section along with the continuous white line on panel D through the endolymphatic sac. The proximal side of the endolymphatic sac is covered by a bony canal called the vestibular aqueduct, along with the endolymphatic duct. In the distal side, the endolymphatic sac, surrounded by conjonctive tissue (CT), extends and protrudes to the outside of the bony labyrinth and is sandwiched between the dura mater (DM) and sigmoid sinus with the squamous part of the temporal bone (TB).
(F) A fine needle is used to cut around the endolymphatic sac (following the dotted yellow lines on panel D).
(G) The preparation is carefully removed from the temporal bone by holding the tissue at the position shown by the asterisk (*, also shown in panel E) and peeling it up.
(H) An isolated whole endolymphatic sac with surrounding tissues.
(I) Schematic version of this isolated endolymphatic sac with surrounding tissues.
(J) Isolated endolymphatic sac without surrounding tissues.
Scale bars: 2 mm (B), 1 mm (J). Please click here to view a larger version of this figure.

Figure 2. Dissection of the opened endolymphatic sac of a P5 wild type mouse.
(A) On step 2.4, the incision line on the vestibular aqueduct is positioned slightly anterior (red dotted line) to make an incision into the endolymphatic sac lumen.
(B) Hold the stem part of the preparation, insert a 27-gauge needle into the lumen, and move it to cut the endolymphatic sac into two sheets.
(C) Schematic illustration of panel B.
(D) Hold the edge of each sheet with forceps and separate them from each other.
(E) Schematic illustration of panel D.
(F) The endolymphatic sac is separated into two sheets, including the epithelium and the surrounding tissues. Please click here to view a larger version of this figure.

Figure 3. Dissection of R26LSL-RCL-tdT/+;Tg(ATP6V1B1-Cre)1Rnel/Mn mouse endolymphatic sac at E16.5, P5, and P30. All images presented show tdTomato fluorescence obtained using a stereomicroscope with a 1 x objective equipped for detection of tdTomato fluorescence.
(A, B) Mid-sagittal section of the skull of a E16.5 R26LSL-RCL-tdT/+;Tg(ATP6V1B1-Cre)1Rnel/Mn mouse before (A) and after (B) half-brain removal. tdTomato fluorescence outlines the position of the inner ear. The endolymphatic sac is readily visible even without dissection (arrowhead).
(C, E, G) Isolated inner ears from E16.5, P5 and P30 mice, respectively.
(D, F and H) Higher magnification images of the corresponding microdissected endolymphatic sacs and ducts. At P30, the endolymphatic duct is encapsulated in bone making it particularly difficult to isolate. Scale bars: 2 mm (A, B, C, E, G), 500 µm (D, F, H). Please click here to view a larger version of this figure.

Figure 4. Gross anatomy of the otic capsule with an enlarged endolymphatic sac. Inner ears from Slc26a4+/- (left) and Slc26a4-/- (right) mouse littermates at P105. The vestibular aqueduct and endolymphatic sac and duct (black dotted lines) are enlarged in the Slc26a4-/- mouse as compared to those in a Slc26a4+/- mouse. Scale bar: 2 mm. Please click here to view a larger version of this figure.

Figure 5. SLC26A4 expression of mitochondria-rich cells in the endolymphatic sac epithelium at E16.5 and P5.
(A, B) Isolated endolymphatic sac from E16.5 mouse labeled with anti-SLC26A4 antibody (green) and phalloidin which labels β-actin (ACTB, red).
(C) A low-magnification image of opened endolymphatic sac from P5 mouse labeled with an anti-SLC26A4 antibody (green). Phalloidin (ACTB, red) can be used to highlight the presence of the endolymphatic sac as well as the conjunctive tissue around it.
(D) Isolated endolymphatic sac labeled with an anti-SLC26A4 antibody (green).
(E) Schematic illustration of endolymphatic sac epithelium highlighting the presence of two cell types: the mitochondria-rich cells, which apical surface is covered with microvilli, and the ribosome-rich cells.
(F-G) High-magnification images of endolymphatic sac epithelium at P5, after the endolymphatic sac was opened and labeled with an anti-SLC26A4 antibody (green) and phalloidin (ACTB, red). A representative image at the apical membrane level is shown in G, and a reconstructed cross-section from z-stack at the level of the punctate white line is shown in F. The nucleus of the cells is labeled with DAPI (blue).
Scale bars: 100 μm (A, B); 200 μm (C, D) ; 20 μm (F, G). Please click here to view a larger version of this figure.
Supplementary Figure 1. Incident light and corresponding tdTomato fluorescence images of a P5 R26LSL-RCL-tdT/+;Tg(ATP6V1B1-Cre)1Rnel/Mn mouse inner ear at three steps of the dissection. The endolymphatic sac and duct can be readily visualized using tdTomato fluorescence.
(A-B) Region of the inner ear in the posterior part of an intact half skull of a P5 R26LSL-RCL-tdT/+;Tg(ATP6V1B1-Cre)1Rnel/Mn mouse.
(C-D) Removal of the skin and part of the skull allows better visualization of the region of the endolymphatic sac.
(E, F) Isolated inner ear with the endolymphatic sac still associated with conjunctive tissue.
(A, C, E) Images captured in incident light. (B, D, F) tdTomato fluorescence of the corresponding tissue. Scale bars: 2 mm (A-B), 1 mm (C-F). Please click here to download this File.
Supplementary Figure 2. Comparison of the fluorescence of isolated endolymphatic sacs of R26LSL-RCL-tdT/+;Tg(ATP6V1B1-Cre)1Rnel/Mn and R26LSL-RCL-tdT/+ littermate mice at E16.5 and P5. tdTomato fluorescence greatly facilitates the recognition of the endolymphatic sac and duct.
(A-C) Microdissected endolymphatic sacs of E16.5 R26LSL-RCL-tdT/+;Tg(ATP6V1B1-Cre)1Rnel/Mn (A) and R26LSL-RCL-tdT/+ littermate mice (B, C).
(D-F) Microdissected endolymphatic sacs of P5 R26LSL-RCL-tdT/+;Tg(ATP6V1B1-Cre)1Rnel/Mn (D) and R26LSL-RCL-tdT/+ littermate mice (E, F).
(A, B, D, E) tdTomato fluorescence. (C, F) Incident light images corresponding to B and E. Scale bars: 500 μm. Please click here to download this File.