Auditory Brain Atlas


Preliminary assays of gene expression using the CLARITY technique

CLARITY for mapping the nervous system. Chung K and K Deisseroth. Nature Methods 10(6), 508-513 (June 2013).
Structural and molecular interrogation of intact biological systems. Chung K, Wallace J, Kim SY, Kalyanasundaram S, Andalman AS, Davidson TJ, Mirzabekov JJ, Zalocusky KA, Mattis J, Denisin AJ, Pak S, Bernstein H, Ramakrishnan C, Grosenick L, Gradinaru V, and K Deisseroth.
Nature 497, 332–337 (16 May 2013).

The data presented in this section are the results of preliminary experimentation with the CLARITY method of brain tissue fixation and clearing. Data collected in collaboration with Wei Guo in the Polley Laboratory.

Example 1
  • Adult mouse brain (split hemispheres)
  • Choline acetyltransferase EYFP fluorescence

Split hemispheres (after clearing)

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Image: Adult mouse cleared using CLARITY procedure.
Markers: ChAT EYFP fluorescence (not visible).

ChAT EYFP fluorescence

Stacks Image 2555
Image: Confocal sections from nucleus basalis imaged in intact left hemisphere (25x immersion objective).
Markers: ChAT EYFP (green).

ChAT EYFP + Cholera Toxin

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Image: 40 um horizontal sections through nucleus basal of ChAT EYFP mouse colabeled with cholera toxin subunit B retrograde tracer injection into primary auditory cortex (A1).
Markers: ChAT EYFP (green); Alexa 594-conjugated cholera toxin B (red)

Top (montage): low magnification horizontal section at the level of the nucleus basal is showing CTB injection into A1 and location of labeled cells (inset).
Middle (10x, 20x): yellow circles indicate locations of cells labeled by ChAT and/or CTB, shown at higher magnification in two bottom panels.
Bottom rows: yellow arrows show double-labeled ChAT/CTB cells. Note that some CTB cells do not colocalize with ChAT.