README: Local activation of CA1 pyramidal cells induces theta phase precession

https://doi.org/10.5061/dryad.1c59zw431

This dataset encompasses extracellular recordings obtained from freely-moving mice, integral to the research presented in our manuscript entitled “Local activation of CA1 pyramidal cells induces theta phase precession”. The data are available at two levels of processing.

1.    Processed data: MATLAB variable files containing details regarding each putative pyramidal cell (PYR) and interneuron (INT) described in the manuscript. These consist of:

• CA1_units.mat: including 1,095 PYRs and 329 INTs recorded from hippocampal region CA1.
• PPC_units.mat: including 195 PYRs recorded from the posterior parietal cortex (PPC).

2. Raw data: Neuronal and auxiliary data recorded during every experimental session. The data include 69 sessions from CA1 and 22 sessions from the PPC. Files from every session are compressed into a .zip file carrying the session name. A list of each session, the animal it was recorded from, and the recorded brain region is available in a separate table.

Description of the data and file structure

Processed data

Each of these two files contains structures with information on all the units used to generate the results in the manuscript. The files include only well-isolated units that were active and stable on the linear track, as detailed in the Materials and Methods section of the manuscript. Within every field of the structure r, each row corresponds to a single unit. The fields are:

-       session: The session during which the unit was recorded.

-       shankclu: The shank on which the unit was recorded (column 1) and the cluster (unit) number on the shank (column 2).

-       type: The cell type: 0, INT; 1, PYR.

-       depth: Depth of the unit within the pyramidal layer [μm]. Depth is defined only for a subset of units, as detailed in the Materials and Methods; for other units, the value is NaN.

-       spk_width: Spike width [ms].

-       burst_index: Burst index.

-       Iact: Number of postsynaptic units.

-       InhbMe: Number of presynaptic INTs.

-       Illum_dist: The horizontal distance between the shank to which the optical fiber employed for on-track illumination is coupled, and the shank on which the unit was recorded. 0, Same shank; 0.1, In dual-sided probes, the other side of the same shank; 1. One shank away; 1.1, In dual-sided probes, the other side of the adjacent shank; 2, Two shanks away; 3, Three shanks away.

-       illumP: Peak illumination power on the track [μW].

-       illumInt: Estimated peak light intensity at the estimated location of the soma [mW/mm2].

-       off_lg_gain: Gain in firing rate during illumination in the home cage (off the linear track).

-       lg_lim: Spatial limits of illumination [cm].

-       lg_gain: Firing rate gain during on-track illumination.

-       lg_gain_pval: P-value for an increase in firing rate during on-track illumination.

-       lgf_act: Binary flag (0/1) for units that increase their firing rate during on-track illumination.

-       lgf_art_field: Binary flag for units exhibiting an artificial field.

-       lgf_rate_amp: Binary flag for units exhibiting a significant rate increase during Light trials. Units with artificial fields are not included (receive 0).

-       lgf_frate_dec: Binary flag for units exhibiting a significant rate decrease during Light trials.

-       lg_fNC: Binary flag for units that do not exhibit a significant change in firing rate during Light compared with Control trials.

-       co_bsFR: Baseline firing rate on track during Control and Return trials.

-       co_spontFields: Number of spontaneous place fields that appear during Control and Return trials.

-       co_spontTPP: Binary flag for the occurrence of spontaneous precession within one of the spontaneous fields appearing during Control or Return trials.

-       co_SI: Spatial information during Control trials [bit/spk].

-       co_fieldSelec: Field selectivity for the illuminated region during Control trials.

-       co_lglim_mFR: Mean firing rate within illumination limits during Control trials [spk/s].

-       lg_SI: Spatial information during Light trials [bit/spk].

-       lg_fieldSelec: Field selectivity for the illuminated region during Light trials.

-       lg_lim_mFR: Mean firing rate within illumination limits during Light trials [spk/s].

-       lgf_iTPP: Binary flag for artificial fields with synthetic precession in either the spatial or temporal domain.

-       lgf_sp_iTPP: Binary flag for artificial fields with synthetic spatial precession.

-       lgf_te_iTPP: Binary flag for artificial fields with synthetic temporal precession.

-       lg_sp_TPP: Four properties of spatial precession during Light trials:

1. a: Slope [cyc/cm].
2. R: Fit to slope.
3. ηs: Spatial precession effect size.
4. Spatial precession occurance binary flag.

-       lg_tm_TPP: Three properties of temporal precession during Light trials:

1. Spike frequency relative to LFP.
2. ηt: Temporal precession effect size.
3. Temporal precession occurrence binary flag.

Raw data

For every session, the zip file consists of multiple files, describing neuronal spike timing (clu and res files), local field potentials LFP and auxiliary data (an eeg file), animal movement and trial structure (trl and trlstm files), and other useful information for working with the dataset (xml and prm.xml files). The clu, res, and eeg files correspond to the format described in Hazan et al., 2006, Journal of Neuroscience Methods. The files are:

-.res. files: ASCII files recording spike times, in samples per shank, sampled at 20 kHz. For instance, the file 'mDS2_20.res.1' contains spike times from the first shank recorded during session 'mDS2_20'.

-.clu. files: ASCII files corresponding to the res files. These files label the spike units. The first element in every clu file denotes the total number of recorded units.

-.eeg file: Binary (16 bit) files that contain the data sampled at 1250 Hz. These files incorporate both extracellular (neuronal) and auxiliary channels, such as those used for monitoring position in real time and the current applied to the on-head diodes during light stimulation.

-.xml file: Each .xml file provides the meta-information necessary for interpreting the .eeg file. This includes details on the number of channels, sampling rates, and other technical specifications.

-.prm.xml file: Contains additional metadata specific to each recorded channel, elaborating details related to the auxiliary channels.

-.trl file: A MATLAB structure containing information regarding the position and speed of the animal and linear track trial structure. This file includes the following variables:

• tmov: A structure with animal movement parameters, sampled at 20,000/512 = 39.0625 Hz.

  • spd: Animal running speed, [cm/s].
  • dir: Animal running angle, [rad].
  • ang: The angle of the head of the animal.
  • tidx: Time index in the eeg file.

• pos_dirs: The linearized position of the animal along the track, sampled at the movement sampling frequency. The first column contains the distance, in cm, from the right edge of the linear track, used for trials where the animal runs from right to left (marked as "1" in the trials variable). The second column contains the position in relation to the left edge of the linear track used for the return trials (marked as "2" in the trials variable).

• trials: Each row corresponds to a linear track trial. The columns correspond to:

1. Trial start at movement sampling frequency (39.0625 Hz).
2. Trial end at movement sampling frequency (39.0625 Hz).
3. Running direction (1 – right to left, 2 – left to right).
4. Trial start at spiking sampling frequency (20 kHz).
5. Trial end at spiking sampling frequency (20 kHz).
6. Optogenetic stimulation trial flag (1 – trial with stimulation, 0 – without).

-.trlstm file: This MATLAB file contains information regarding linear track trial structure and optogenetic stimulation. Each file contains a structure with the following fields:

• LT_stimCh: Channel/s recording the current applied to the diodes used for illumination on the track, numbered 1-6.
• stim_channels: Channel/s recording the current applied to the diodes used for illumination, numbered as in the .eeg and .xml files.
• nstimCh: Number of channels used for recording the current on the track.
• stim_targets: The shank/s to which fibers used for illumination on the track were coupled to (i.e., the target shanks).
• stim_dirs: The running direction in which illumination occurred, corresponding to the third column of the trials variable in the .trl file.
• tr_rmv: Binary flag for trials removed from analysis due to weak or irregular stimulation, corresponding to the rows of the trials variable.
• stim_lims: Spatial limits of illumination, [cm].
• analogmap: 3D array reporting the illumination in every spatial bin at every trial (trials x spatial bins x stimulation channels), [μW]. This variable contains all available stimulation channels, including those not employed for illumination on the track. For example, if the variable LT_stimCh=2, illumination would occur at analogmap( trials(:,6), :, 2 ).
• binC: Centers of spatial bins used for analogmap, [cm].
• edges: Edges of spatial bins used for analogmap, [cm].