DOI: 10.5061/dryad.66t1g1k2w
title: Patch-clamp recordings from dorsal raphe neurons

description: This dataset contains whole-cell electrophysiological recordings
 (patch-clamp recordings) from three cell types in mice: serotonin (5-HT)
 neurons, somatostatin (SOM)-expressing GABA interneurons, and layer 5
 pyramidal neurons. 5-HT and GABA neurons were recorded in the dorsal raphe
 nucleus (DRN), which is the main source of serotonergic input to the
 forebrain. Together, they make up the majority of the neurons found in the
 DRN. This dataset can be used to investigate the intrinsic
 electrophysiological properties of these two types of DRN neurons and
 contrast them with another abundant and well-studied cell type, the L5
 pyramidal neuron. This data was used in our paper describing a spiking
 neural network model of the dorsal raphe nucleus: Emerson F. Harkin,
 Michael B. Lynn, Alexandre Payeur, Jean-François Boucher, Léa
 Caya-Bissonnette, Dominic Cyr, Chloe Stewart, André Longtin, Richard Naud,
 and Jean-Claude Béïque. Temporal derivative computation in the dorsal
 raphe network revealed by an experimentally-driven augmented
 integrate-and-fire modeling framework. eLife, 2023. doi:
 10.7554/eLife.72951
description: Recordings were carried out in 4-8 week old C57/Bl6 mice.
 SERT-Cre::Rosa-TdTomato and SOM-Cre::Rosa-TdTomatotransgenic lines were
 used to fluorescently label DRN 5-HT and SOM GABA neurons, respectively.
 All experiments were carried out in accordance with procedures approved by
 the University of Ottawa Animal Care and Veterinary Services.
 Experiments were carried out at room temperature using a
 potassium-gluconate-based internal solution, except for synaptic
 physiology experiments for which a cesium-based solution was used. In all
 cases, the external solution consisted of standard artificial
 cerebrospinal fluid. Detailed information is available
 in our related publication. The data is laid out as
 shown below, with recordings from DRN 5-HT, DRN GABA, and L5 mPFC
 pyramidal neurons stored in the corresponding directories.
 <pre> . ├── 5HT │   ├── current_steps │   ├── GABA_synapses │   ├──
 gating │   ├── heated_gating │   ├── heated_pharmacology │   ├──
 long_curr_steps │   ├── membrane_parameters │   ├── OU_noise │   ├──
 OU_noise_heated │   ├── pharmacology │   └── spk_time ├── GABA │   ├──
 current_steps │   ├── DRN393_firing_vsteps │   ├── DRN398_firing_vsteps
 │   ├── long_curr_steps │   ├── matched_I_V_steps │   ├──
 membrane_parameters │   ├── OU_noise │   ├── spk_time │   └──
 unmatched_V_steps └── mPFC ├── current_steps ├── gating └── OU_noise
 </pre> The names of subdirectories mainly reflect the
 different types of experiments carried out in each cell type:
 <code>current_steps</code>: Short (~1s)
 steps of current applied in current clamp. 
 <code>long_curr_steps</code>: 20-30s current steps.
 <code>spk_time</code>: A 1s hyperpolarizing current
 step of variable amplitude followed by a short depolarizing step to evoke
 spiking. This protocol has been used in the past to
 investigate an effect of inactivating potassium currents (eg IA) on spike
 timing. 
 <code>OU_noise</code>: Frozen Ornstein-Uhlenbeck noise with
 various timescale and amplitude characteristics applied in current clamp.
 This protocol provides a rich dataset for training
 spiking neuron models (see <strong>Related
 works</strong>). Each experiment is divided
 into <em>training</em> and <em>test</em> portions
 which we recommend using for training and testing models,
 respectively. 
 <code>gating</code>: Voltage clamp protocol designed to
 characterize the voltage-dependence of ionic currents that activate near
 spike threshold. Consists of a hyperpolarizing pulse followed by
 depolarizing steps of varying amplitude. These
 experiments were carried out in the presence of tetrodotoxin (TTX) to
 block voltage-gated sodium channels. In the GABA
 dataset, these experiments are split across the
 <code>unmatched_V_steps</code>,
 <code>matched_V_steps</code>, and
 <code>DRN39X_firing_vsteps</code> directories because in some
 cases we were able to carry out <code>spk_time</code> and
 <code>gating</code> experiments in the same cells. In the case
 of <code>DRN39X_firing_vsteps</code>, we carried out the
 <code>spk_timing</code> protocol, applied TTX, then carried
 out the <code>gating</code> protocol. In the case of
 <code>matched_I_V_steps</code>, both protocols were carried
 out in the presence of TTX. 
 <code>pharmacology</code>: Voltage clamp protocol designed to
 activate voltage-dependent ionic currents.
 <code>18411010.abf</code> was recorded under baseline
 conditions, <code>18411013.abf</code> was recorded in the
 presence of TEA, and <code>18411015.abf</code> was recorded in
 the presence of TEA + 4AP. All three recordings were carried out in the
 same cell. 
 <code>membrane_parameters</code>: Passive membrane parameters
 (resistance and capacitance) of DRN neurons. 
 Most of the data files included in this package are
 electrophysiological recordings stored in Axon binary format (ABF) which
 can be opened in Python using neo or ez-ephys (which itself uses neo internally). Recordings are named according to the following convention: <pre><code>&lt;experimenter_prefix&gt;&lt;YYMDD&gt;&lt;id&gt;.abf</code></pre> where <code>&lt;experimenter_prefix&gt;</code> is an optional prefix with the initials of the person who collected the data, <code>&lt;YYMDD&gt;</code> is the date the experiment was carried out (<code>M</code> is either a number representing a month between January and September, or one of the letters <code>o</code>, <code>n</code>, or <code>d</code> for the remaining months), and <code>&lt;id&gt;</code> is a three digit number. For example, <code>JF19121013.abf</code> was collected by Jean-François Boucher on January 21, 2019. Metadata is included in files named <code>index.csv</code>. These tables include a unique ID for each neuron recorded (this can be used to determine which recordings were carried out in the same neuron), the passive membrane resistance in MOhm (R), membrane capacitance in pF (C), and the holding current at -70 mV or -60 mV in pA (<code>I_hold</code>). <code>checksums.txt</code> includes SHA256 checksums that can be used to verify data integrity.
description: See the included <code>README.md</code> for detailed
 information about the dataset.