DOI: 10.6084/m9.figshare.6739514.v1
title: Electrophysiological Profiling of Neocortical Neural Subtypes: The in-Vivo whole cell patch-clamp data

description: The Animal Experiment Committee of RIKEN BSI (Brain Science Institute; http://www.brain.riken.jp/en/ ) approved the entire experimental procedures. Being in accordance with the guidelines of the committee, they were performed on urethane anesthetized mice. The data and experimental protocol presented in this paper are the same as our recent publication (Safari et al., 2017). It is briefly summarized here. The entire data was recorded from three types of transgenic mouse lines in which PV, SST or whole GABAergic interneurons express Channelrhodopsin-2(ChR2). The following three lines of transgenic mice used in this study:<br><br> <br>1. VGAT-ChR2-YFP mice, B6. Cg-Tg(Slc32a1-COP4*H134R/EYFP)8Gfng/J).<br>2. SST-ChR2-YFPmice, STOCK SST J × B6;129S-Gt(ROSA)26Sortm32 (CAG-COP4*H134R/EYFP) Hze/J.<br>3. PV-ChR2-YFP mice, B6;129P-Pvalbtml (cre)Arbr/J × B6;129S-Gt(ROSA)26Sortm32(CAG COP4*H134R/EYFP) Hze/J.<br> <br>Urethane (1.5–1.9 mg/g body weight), with additional doses if necessary was used to anesthetize the animals. A small custom-made head chamber attached over the occipital region of the left hemisphere, was used to immobilize the animal’s head under a two-photon microscope. After removing a small part of the skull and dura mater over the primary visual cortex, the exposed cortex was covered with agarose (1.5–2.0% in Ringer’s solution).<br><br><br>The membrane potentials were recorded using double Whole-cell current-clamp simultaneously from YFP-positive interneurons (PV or SST-positive interneurons) and nearby pyramidal (YFP-negative neurons with large soma of pyramidal shape and large apical dendrites) neurons. They were recorded at a depth of 110–230 μm of the cortical surface. The average distances between the PV - SST was 28 ± 5.0 μm while it was 36 ± 6.0 μm for PV- Pyr cell pairs. The multi-clamp amplifier (Multiclamp 700B) was used for recording, and the data was sampled at 20 kHz. Recordings were digitized using NI-DAQ board (PCI-MIO-16E-4, National Instruments) and acquired using custom-made LabVIEW software. <br>Safari, M.-S., Mirnajafi-Zadeh, J., Hioki, H., and Tsumoto, T. (2017). Parvalbumin-expressing interneurons can act solo while somatostatin-expressing interneurons act in chorus in most cases on cortical pyramidal cells. <i>Scientific Reports</i> 7(1), 12764. doi: 10.1038/s41598-017-12958-4.<br><br>We uploaded the data (raw data in compressed Matlab format as well as processed data in SPSS format) and a demo program for the cell type identification. The sampling time is 20 kHz and the units are in mV in the dataset. The data is in the Matlab mat file format. The GUI is compatible with the Matlab ver 2015b or later. Files PV.zip, Pyr.zip and SST.zip contain different cell types. The file "Demo.zip" contain the entire files needed to run the demo. Moreover, the complete code of the algorithm was uploaded as "complete_code.zip". When unzipped, and changing the current directory to its address, running "main.m" will perform the entire identification task and reports the results and displayed the performance charts. <br>order to assess the performance of our method on other experiments such as in vitro whole cell recording, the program was further tested on the pool of 50 neurons in the Allen Cell Types Database (Allen Cell Types Database, 2015). We used the data from 5 major subtypes of neurons namely as excitatory pyramidal neuron, and four major inhibitory neurons namely as parvalbumin, somatostatin, 5HT3a and the vasoactive intestinal polypeptide (VIP) expressing neurons. Transgenic mice lines Nr5a1-Cre, Pvalb-IRES-Cre, Sst-IRES-Cre, Htr3a-Cre_NO154, and Vip-IRES-Cre were selected to target pyramidal, PV, SST, 5HT3a, and VIP neurons, respectively. We used 10 neurons per each group from layers 2/3,4,5,6a of the cortex. The number of extracted spikes for Pyramidal, PV, SST, 5HT3a, and VIP groups were 334, 721, 447, 378, and 459 respectively.<br><br>Allen Cell Types Database (2015). Cell Types: Overview of the Data. Available at: http://celltypes.brain-map.org /.[Accessed August 31 2018].<br>The exported in vitro dataset and the developed program could be assessed in the file “in_vitro.zip”.<br>Unzip the zip file (in_vitro.zip) to a folder. Run Matlab (ver 2015 or higher). Make the folder as the current directory. Run main.m<br>