DOI: 10.5281/zenodo.6647628
title: Dataset (NWB format) from Gao et al (2018) A cortico-cerebellar loop for motor planning. Nature, Nov;563(7729):113-116.

description: <strong>Summary</strong> These experiments measure neuronal responses from anterior lateral motor cortex (ALM) and deep cerebellar nucleus (CN) of adult mice performing pole location discrimination with a short-term memory. In some cases, we manipulate activity of one brain region while recording from the other region. Dataset: <em>Li N (2018). Extracellular recordings from anterior lateral motor cortex (ALM) and cerebellar nucleus neurons of adult mice performing a tactile decision behavior. </em> Data included in this release: 34 sessions (9 mice), ALM recording during fastigial or dentate photoactivation 20 sessions (4 mice), ALM recording during DCN photoinhibition <em>(Data already available at: </em><em>http://dx.doi.org/10.6080/K0NS0S26</em><em>)</em> 185 sessions (18 mice), CN recording. In some sessions, ALM photoinhibition was tested <em>(Data included in this release. Data is in NWB format).</em> Data from the follow publication: <em>Gao Z, Davis C, Thomas AM, Economo MN, Abrego AM, Svoboda K, De Zeeuw CI, Li N (2018). A cortico-cerebellar loop for motor planning. Nature, Nov;563(7729):113-116. doi: 10.1038/s41586-018-0633-x. Epub 2018 Oct 17.</em> <strong>Animals</strong> This dataset contains data from 31 mice (age &gt; P60, both male and female mice, Supplemental Table 1). 9 C57B1/6 mice were used for ALM recordings during photo-activation of the CN. 4 L7-cre (Lewis et al., 2004) crossed to Ai32 (Rosa26-LSL-ChR2-EYFP, JAX Stock#012569) (Madisen et al., 2012) mice were used for ALM recordings during CN photo-inhibition. 10 C57B1/6 mice were used for CN recording experiments. 8 VGAT-ChR2-EYFP mice (Jackson laboratory, JAX Stock#014548) (Zhao et al., 2011) were used for CN recordings during ALM photo-inhibition. <strong>Experimental methods</strong> Detailed experimental methods are described in the manuscript (Gao et al 2018). <strong><em>Behavior</em></strong> Mice measured the location of an object using their whiskers during a sample epoch (1.3 s) (O'Connor et al., 2010). After the sample epoch they must hold their decision about object location in memory for a delay period (1.3 s) (Guo et al., 2014). At the end of the delay period, an auditory cue (0.1) instructed the mice to report their decision with directional licking (“lick left”/”lick right”). <strong><em>CN ChR2 photo-activation </em></strong> For ChR2 photo-activation of the CN, wild-type mice injected with AAV2-hSyn1-(h134R)ChR2-EYFP virus were used. Light from a 473 nm laser (Laser Quantum, Part# Gem 473) was controlled by an acousto-optical modulator (AOM; Quanta Tech) and a shutter (Vincent Associates). To prevent the mice from distinguishing photostimulation trials from control trials using visual cues, a ‘masking flash’ was delivered using 470 nm LEDs (Luxeon Star) near the eyes of the mice. The masking flash began as the pole started to move and continued through the end of the epoch in which photostimulation could occur. The photostimulus was pulses of light (5 ms pulse duration) delivered at 20 Hz and a range of peak powers (5, 10, 15mW). The power values reported in the paper indicate average powers (0.5, 1, 1.5 mW). The powers were measured at the fiber tip. The photostimulus started at the beginning of a task epoch and continued for 0.455 s (10 pulses). <strong><em>CN photo-inhibition</em></strong> In L7-cre × Ai32 mice, ChR2 was expressed in cerebellar Purkinje cells. We photostimulated Purkinje cells to inhibit neurons in the CN. The photostimulus was a 40 Hz sinusoid (average power, 4.5 mW) lasting for 1.3 sec, including a 100-200ms linear ramp during the laser offset to reduce rebound neuronal activity. <strong><em>ALM photo-inhibition</em></strong> ALM is centered on bregma anterior 2.5 mm, lateral 1.5 mm (Chen et al., 2017; Guo et al., 2014; Li et al., 2016). For photo-inhibition of ALM, we photostimulated cortical GABAergic neurons in VGAT-ChR2-EYFP mice (8 mice). Photostimulation was performed through the clear-skull cap implant by directing the blue laser over the skull (beam diameter: 400 µm at 4σ, bregma anterior 2.5 mm, lateral 1.5 mm). The light transmission through the intact skull was 50% (Guo et al., 2014). We photo-inhibited ALM for 1.3 s at the beginning of the delay epoch, including a 100 ms linear ramp at the laser offset to minimize rebound excitation. This photostimulus was empirically determined to produce robust photo-inhibition in ALM (Guo et al., 2014; Li et al., 2016). The photo-inhibition silenced 90% of spikes in a cortical area of 1mm radius (at half-max) through all cortical layers. For unilateral ALM photo-inhibition, we used a 40 Hz sinusoidal photostimulus (1.5mW average power at the skull surface) at 2.5 mm anterior and 1.5 mm lateral from bregma. For bilateral ALM photo-inhibition, we used a constant photostimulus and a scanning galvo (GVSM002, Thorlabs), which stepped the laser beam sequentially through the photo-inhibition sites at the rate of 1 step per 5 ms (step time: 0.2 ms; dwell time: 4.8 ms; measured using a photodiode). 8 photo-inhibition sites were spaced in 1 mm at anterior 2-3 mm and lateral 1-2 mm from bregma, covering ALM. Peak power was adjusted based on the number of photo-inhibition sites to achieve 1.5 mW average power per site. <strong><em>Electrophysiology</em></strong> Extracellular spikes were recorded using 32-channel NeuroNexus silicon probes (Part# A4x8-5mm-100-200-177) or 64-channel Cambridge NeuroTech silicon probes (H2 acute probe, 25 µm spacing, 2 shanks). The 32-channel voltage signals were multiplexed, digitized by a PCI6133 board at 400 kHz (National Instruments) at 14 bit, demultiplexed (sampling at 25,000 Hz) and stored for offline analysis. The 64-channel voltage signals were amplified and digitized on an Intan RHD2164 64-Channel Amplifier Board (Intan Technology) at 16 bit, recorded on an Intan RHD2000-Series Amplifier Evaluation System (sampling at 20,000 Hz) using Open-Source RHD2000 Interface Software from Intan Technology (version 1.5.2), and stored for offline analysis. The extracellular recording traces were band-pass filtered (300-6 kHz). Events that exceeded an amplitude threshold (4 standard deviations of the background) were subjected to manual spike sorting to extract single-units (Guo et al., 2014). <strong>Data analysis</strong> For ALM recordings, units are classified based on spike shape. Spike widths were computed as the trough-to-peak interval in the mean spike waveform. Units with spike width &lt; 0.35 ms were defined as fast-spiking neurons (82/1309) and units with spike widths &gt; 0.45 ms as putative pyramidal neurons (1194/1309). Units with intermediate values (0.35 - 0.45 ms, 33/1309) were excluded from analyses. This classification was previously verified by optogenetic tagging of GABAergic neurons (Guo et al., 2014). For CN recordings, units are classified based on recording location. We estimated unit locations based on recording track labeling, recording depth, and the lamination of activity patterns across the recording shanks. In <em>post-hoc</em> histology, CN boundaries were visible in DAPI staining. <strong>References</strong> Chen, T.W., Li, N., Daie, K., and Svoboda, K. (2017). A Map of Anticipatory Activity in Mouse Motor Cortex. Neuron<em> 94</em>, 866-879 e864. Guo, Z.V., Li, N., Huber, D., Ophir, E., Gutnisky , D.A., Ting, J.T., Feng, G., and Svoboda, K. (2014). Flow of cortical activity underlying a tactile decision in mice. Neuron<em> 81</em>, 179-194. Lewis, P.M., Gritli-Linde, A., Smeyne, R., Kottmann, A., and McMahon, A.P. (2004). Sonic hedgehog signaling is required for expansion of granule neuron precursors and patterning of the mouse cerebellum. Dev Biol<em> 270</em>, 393-410. Li, N., Daie, K., Svoboda, K., and Druckmann, S. (2016). Robust neuronal dynamics in premotor cortex during motor planning. Nature. Madisen, L., Mao, T., Koch, H., Zhuo, J.M., Berenyi, A., Fujisawa, S., Hsu, Y.W., Garcia, A.J., 3rd, Gu, X., Zanella, S.<em>, et al.</em> (2012). A toolbox of Cre-dependent optogenetic transgenic mice for light-induced activation and silencing. Nature neuroscience<em> 15</em>, 793-802. O'Connor, D.H., Clack, N.G., Huber, D., Komiyama, T., Myers, E.W., and Svoboda, K. (2010). Vibrissa-based object localization in head-fixed mice. The Journal of neuroscience : the official journal of the Society for Neuroscience<em> 30</em>, 1947-1967. Zhao, S., Ting, J.T., Atallah, H.E., Qiu, L., Tan, J., Gloss, B., Augustine, G.J., Deisseroth, K., Luo, M., Graybiel, A.M.<em>, et al.</em> (2011). Cell type-specific channelrhodopsin-2 transgenic mice for optogenetic dissection of neural circuitry function. Nature methods<em> 8</em>, 745-752.