Brainstem control of vocalization and its coordination with respiration
Data files
Aug 22, 2024 version files 13.27 GB
Abstract
Phonation critically depends on precise controls of laryngeal muscles in coordination with ongoing respiration. However, the neural circuit mechanisms governing these processes remain unclear. Here, we identified excitatory vocalization-specific laryngeal premotor neurons located in the retroambiguus nucleus (RAmVOC) in adult mice as both necessary and sufficient for driving vocal-cord closure and eliciting mouse ultrasonic vocalizations (USVs). The duration of RAmVOC-activation can determine the lengths of both USV syllables and concurrent expiration periods, with the impact of RAmVOC-activation depending on respiration phases. RAmVOC-neurons receive inhibition from the preBötzinger complex, and inspiration-needs override RAmVOC-mediated-vocal-cord closure. Ablating inhibitory synapses in RAmVOC-neurons compromised this inspiration gating of laryngeal adduction, resulting in discoordination of vocalization with respiration. Our study revealed the hitherto unknown circuits for vocal production and vocal-respiratory coordination.
README: Brainstem control of vocalization and its coordination with respiration
https://doi.org/10.5061/dryad.vmcvdnd0m
Description of the data and file structure
Brainstem control of vocalization and its coordination with respiration
https://doi.org/10.5061/dryad.vmcvdnd0m
DATA used in this study is shared in this depository.
Description of the data and file structure
Each jupyter notebook and .jl file has description regarding data and file structure
USV stands for Ultrasonic Vocalization
Folders
Codes
Julia programming codes for data acquisition and analysis used in this study.
: for acquisition
Nidaq_read.jl, plot_functions.jl
: for analysis
respiration.jl, usvanalysis.jl, usvdetection.jl, USVpreprocess.jl, usv_temp.jl
Fig. 1
This folder is empty (nothing shared)
Fig. 2
Fig. 2C
- Fig. 2C - RAmVOC - preLMN - AllenCCF.ipynb : jupyter notebook for creating data here
- NS-RV1, NS-RV2, NS-RV3.txt: .csv files include name (brain region names), acronym, AP (anterior-posterior)_location, DV (dorsal-ventral)_location, ML (middle-lateral)_location, avIndex (arbitrary number) for 3d Coordinates, units in (mm)
Fig. 2E
- Fig_2_E_RAmVOC-HCR.xlsx: the number of counts for in-situ data (the total numbers of cells (e.g., 24 cells) used in the analysis)
- RAmVOC HCR.ipynb: jupyter notebook file for creating data here
Fig. 2G
- Fig_2_G_GFP_TeLC.h5: .h5 file includes 2d matrix of floats number
- Fig. 2G - representative spectrogram - control - TeLC: jupyter notebook file for creating data here
Fig. 2H
- Analyze_vocalizations_KAT_noStops, ImportWAV_Katie_filter25to110kHz.m: MATLAB codes for analysis here.
- Control_after, Control_before, TeLC_after, TeLC_before.mat : for processed data from MATLAB
- Fig. 2H-I.ipynb: jupyter notebook file for creating data here
- Raw_audio (folder): containing raw .wav files for each group (GFP vs TeLC)
Fig. 2KL
- Fig. 2KL - Squeak - headfix - tailpinch.ipynb: jupyter notebook file for creating data here
- DATA (folder): .jld files containing 1d audio signals
Fig. 3
- Fig. 3GI: jupyter notebook file for creating data here
Fig. 3GI
- DATA (folder)
- female:
- .jld files includes bound information (rectangle; x scale, y scale)
- .h5 files for raw data including 1d audio signal
- Rs:
- .jld files includes bound information (rectangle; x scale, y scale)
- utf:
- .jld files includes bound information (rectangle; x scale, y scale)
- female:
Fig. 3H
- USVs: a folder of images of ultrasonic vocalization syllables
Fig. 4
- Fig. 4 DE, Fig. 4 IK.ipynb: jupyter notebook files for creating data here
Fig. 4DE
- PostIns (folder):
- .h5 files containing raw data
- USV (folder)
- .h5 files containing raw data of breathing and audio signals
- .jld files containing bounding boxes for USV detection
Fig. 4GH
- Fig4GH.jl: .jl file for creating data here
DATA (folder)
- .h5 files containing raw data of breathing and audio signals
- .jld files containing bounding boxes for USV detection
Fig. 4IK
- group (folder)
- Rs (folder):
- .h5 files containing raw data of breathing and audio signals
- Rs_utfs (folder):
- jld files containing bounding boxes for USV detection
- single (folder)
- .h5 files containing raw data of breathing and audio signals
- jld files containing bounding boxes for USV detection
Fig. 5
- Fig. 5 - GFE3 experiments.ipynb: jupyter notebook files for creating data here
Fig. 5 DATA
- GFE3 (folder): each folder (1-5) contains:
- .h5 files containing raw data of breathing and audio signals
- jld files containing bounding boxes for USV detection
- GFP (folder): each folder (1-4) contains:
- .h5 files containing raw data of breathing and audio signals
- jld files containing bounding boxes for USV detection
annotation_volume_10um_by_index.npy: numpy files containing Allen Atlas data frames
Files and variables
File: DATA_deposition.zip
Description: details are available in the README.md
File: README.md
Description: details for DATA_deposition.zip
Access information
Other publicly accessible locations of the data:
- n/a
Data was derived from the following sources:
- n/a