Data from: Impaired hippocampal circuit function underlying memory encoding and consolidation precede robust Aβ deposition in a mouse model of alzheimer's disease
Data files
Sep 19, 2026 version files 1.20 GB
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dryad_2.zip
1.20 GB
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README.md
5.24 KB
Abstract
Current therapeutic strategies for Alzheimer’s disease (AD) target amyloid-beta (Aβ) fibrils and high molecular weight protofibrils associated with plaques, but molecular cascades associated with AD may drive neural systems failure before Aβ plaque deposition in AD. Employing hippocampal electrophysiological recordings and dynamic calcium imaging across the sleep-wake cycle in a freely behaving mouse model of AD before Aβ plaques accumulated, we detected marked impairments of hippocampal systems function: In a spatial behavioral task, phase-amplitude coupling (PAC) of the hippocampal theta and gamma oscillations was impaired and place cell calcium fluctuations were hyper-synchronized with the theta oscillation. These changes were not observed in REM sleep. In subsequent slow wave sleep (SWS), place cell reactivation was reduced. These degraded neural functions underlying memory encoding and consolidation support targeting pathological processes of the pre-plaque phase of AD to treat and prevent hippocampal impairments.
https://doi.org/10.5061/dryad.nk98sf821
This dataset dryad_2.zip contains source data and code for calcium imaging and electrophysiology in CA1 in WT and young APP/PS1 mice.
This work demonstrated that hippocampal dysfunction precedes amyloid-beta plaque formation.
Contact: Hanyan Li, hli51@mgh.harvard.edu
Description of the data and file structure of each file
source_code.m
contains all matlab scripts to generate figures in the manuscript
all scripts for 4 figures in this manuscript. See comments in the script.
calcium.mat
contains calcium traces, positions, timestamps and place cells of wild type and APP/PS1 mice
- wt (wild-type mice), app (APP/PS1 mice)
- name: animal ID
- v1pc.BESTpos: place cell ID when animal run left to right direction
- v1pc.BESTneg: place cell ID when animal run right to left direction
- v1pc.HC.xpos: animal's positions on the linear track that associated with a calcium event (in cm)
- v1pc.HC.vpos: animal's velocity that associated with a calcium event (in cm/s)
- v1pc.HC.t: time of calcium event (relative to start of the recording) (in ms)
- v1pc.HC.tpos: time of calcium event (relative to start of the recording) when animals runs from left to right direction and velocity >1cm/s (in s)
- v1pc.HC.xpos2: animal's positions on the linear track that associated with a calcium event when animals runs from left to right direction and velocity >1cm/s (in cm)
- v1pc.HC.vpos2: animal's velocity on the linear track that associated with a calcium event when animals runs from left to right direction and velocity >1cm/s (in cm/s)
- v1pc.xneg, v1pc.vneg, v1pc.tneg, and v1pc.vneg2 are the same as above except animals is running the other direction.
- v1pc.SIpos: spatial information of each cell (run direction left to right) (in bits/s)
- v1pc.SIneg: spatial information of each cell (run direction right to left) (in bits/s)
- v1pc.pc: unique place cell ID (combined both directions)
- v1pc.nonpc: non- place cell ID
- lap: time of each lap on both directions (in ms)
- onsets: calcium event timestamps associated with different behavior states (in ms)
- pos.T: time on linear track (in ms)
- pos.location: location over time (in cm)
- pos.vel: velocity over time (in cm/s)
- T: length of each behavior's duration (in s)
@runpac_hc_updated.mat
contains hippocampal theta-gamma couplings during run of wild-type mice and app/ps1 mice
- name: animal ID
- runpac_cfc_g: hippocampal theta-gamma coupling measured by cross frequency coherence (cfc) during run behavior, using cerebellum as reference.
- runpac_mi_g: hippocampal theta-gamma coupling measured by modulation index (mi) during run behavior, , using cerebellum as reference.
- age: age in days
@runpac_cort.mat
contains cortical theta-gamma couplings during run of wild-type mice and app/ps1 mice
- runpac_mi_g_cort: cortical theta-gamma coupling measured by modulation index (mi) during run behavior, , using cerebellum as reference.
- runpac_mi_l_cort: cortical theta-gamma coupling measured by modulation index (mi) during run behavior, , using hippocampal local reference.
- age: age in days
@rempac_hc_and_cort.mat
contains theta-gamma couplings during rem sleep of wild-type mice and app/ps1 mice
- name: animal ID
- rempac_mi_g: hippocampal theta-gamma coupling measured by modulation index (mi) during rem sleep, using cerebellum as reference.
- rempac_mi_l: hippocampal theta-gamma coupling measured by modulation index (mi) during rem sleep, using hippocampus local reference.
- rempac_mi_g_cort: cortical theta-gamma coupling measured by modulation index (mi) during rem sleep, using cerebellum as reference.
- rempac_mi_l_cort: cortical theta-gamma coupling measured by modulation index (mi) during rem sleep, using hippocampus local reference.
- age: age in days
swslfp.mat
contains local field potentials during slow wave sleep and timestamps of wild-type mice and app/ps1 mice
- name: ID
- swscort: cortical local field potentials (LFPs) during slow wave sleep (in uV)
- swscell: cell layer LFPs during slow wave sleep (in uV)
- swslfpt: timestamps (in ms)
coh_run_rem.mat
contains calcium trace, and LFPs during run and rem sleep of wild-type mice and app/ps1 mice
- runcoh.nrp: neuropil signal during run (in dff)
- runcoh.dsrunlfp: downsampled LFPs during run (in uV)
- runcoh.IC: each cell's trace during run (in dff)
- remcoh.nrp: neuropil signal during rem (in dff)
- remcoh.dsrunlfp: downsampled LFPs during rem (in uV)
- remcoh.IC: each cell's trace during rem (in dff)
- v1pc: same as in calcium.mat (See above)
- age: age in days
s_mem.csv, table.xlsx and anova_results.csv
contains hypoeractive/hypoactive/normal cells of wild-type mice and app/ps1 mice
data for mixed-effect model and anova tests.
Sharing/Access information
Contact for more questions: Hanyan Li, hli51@mgh.harvard.edu
Code/Software
This MATLAB script was written in 2019b version.