Data from: Reactivation of memory-associated neurons induces downstream suppression of competing neuronal populations
Data files
May 07, 2025 version files 661.76 KB
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firing_rate_day1.csv
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firing_rate_day2.csv
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firing_rate_day3.csv
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M223_licking_data.csv
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M269_licking_data.csv
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M271_licking_data.csv
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M273_licking_data.csv
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M274_licking_data.csv
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M275_licking_data.csv
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M281_licking_data.csv
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M282_licking_data.csv
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M283_licking_data.csv
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M284_licking_data.csv
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M285_licking_data.csv
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M286_licking_data.csv
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README.md
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Abstract
Inducing apparent memory recall by tagging and optogenetically reactivating cells in the hippocampus was demonstrated over a decade ago. However, the hippocampal dynamics resulting from this reactivation remain largely unknown. While calcium imaging is commonly used as a measure of neuronal activity, GCaMP, the most common calcium indicator, cannot be used with optogenetic neuronal reactivation because both require blue light excitation. To resolve this overlap, we demonstrate optogenetic reactivation with a red-shifted opsin, ChrimsonR. We then conduct dual-color calcium imaging in CA1 during memory reactivation in DG. In addition to measuring population dynamics in CA1, CA1 cells tagged during the original experience were identified. In the fear conditioned animals (FC+), non-tagged cells in CA1 decreased their firing rate during stimulation, while tagged cells maintained their activity level. In the FC+ animals, as the behavioral effect of stimulation decreased across days, so did the changes in neural activity during stimulation. Our results both demonstrate the technical feasibility of calcium imaging during optogenetic reactivation of memory-associated neurons and advance our understanding of the dynamics underlying this reactivation.
https://doi.org/10.5061/dryad.xsj3tx9q0
Overview
These data were collected from mouse hippocampus during a behavioral licking task and during optogenetic stimulation. Prior to the behavioral and imaging task, mice were trained to lick from a lick port as much as they'd like during a 15 minute session. Each mouse received one session per day. Additionally, mice had an experience tagged; tagged neurons express mCherry in CA1 and ChrimsonR-mCherry in DG. GCaMP was virally injected to CA1. These datasets are the imaging and behavioral data collected during optogenetic memory reactivation.
Description of the data and file structure
This dataset totally consists of 15 data files (firing rate and mouse licking data). Both behavioral data and imaging data are contained in this dataset. The behavioral data is organized by mouse, while the imaging data is organized by day.
Behavioral Data
The behavioral data correspond with the licking epochs in the described experiment. The epochs were three minutes in length and alternated between no stimulation and stimulation, starting with no stimulation. There was a half second delay after each lick, and the percentages are the percent of time the mouse was licking or in the delay period relative to the 3 minute epoch.
- Each file correspond with a single animal
- Each row corresponds to a day
- The columns are the licking epochs, and the numbers are the percentage of time the mouse spent licking.
Imaging data
The imaging data were collected through a hippocampal window while the mouse was awake and behaving. Neuronal traces were extracted as described below and aggregated across epochs. Each file is a day, and each row represents a cell. The values are the estimated lick rate, which should only be used relative to other estimated lick rates in this experiment. Absolute values are not meaningful. The columns are as follows
- Mouse: The mouse the cell came from
- Day: Which day the experiment took place
- Experimental: Whether the mouse previously received a foot-shock (1) or not (0) during tagging
- mCherry: Whether the cell was identified as expressing mCherry (1), not expressing mCherry (-1) or unable to tell (0)
- All rate: Average firing rate across the trial
- Stim rate: Average firing rate during stimulation epochs
- No stim rate: Average firing rate during the first epoch prior to stimulation
- Post stim rate: Average firing rate during the two epochs after stimulation
- Second stim rate: Average firing rate during the second stimulation epoch
- Third no stim rate: Average firing rate during the third no stimulation epoch, which was the final epoch
- Lick rate: Average firing rate when the mouse was licking
- No lick rate: Average firing rate when the mouse was not licking
- Stim lick rate: Average firing rate when stimulation took place and the mouse was licking
- Stim no lick rate: Average firing rate when stimulation took place and the mouse was not licking
- Second stim lick rate: Average firing rate during the second stimulation epoch and the mouse was licking
- Second stim no lick rate: Average firing rate during the second stimulation epoch and the mouse was not licking
- Third no stim lick rate: Average firing rate during the third no stimulation epoch (the final epoch) and the mouse was licking
- Third no stim no lick rate: Average firing rate during the third no stimulation epoch (the final epoch) and the mouse was not licking
Code/Software
CaImAn was used to process the imaging files. Custom Python code was used to align the mCherry images to the GCaMP activity data and account for bleed-through. All cellular activity traces were manually inspected for sufficient signal and cleaned of motion artifacts.
These data were collected using 2-photon imaging during optogenetic memory reactivation. Behavioral data were collected during imaging.
Calcium transients were extracted using CaImAn as described in the manuscript. The mCherry images were aligned to the imaging data and corrected for any bleed through. Traces were manually inspected to ensure only cells with sufficient signal were included. The available data are the results of this processing, raw data are available upon request.