data and scripts necessary to re-create plots for Dennis2017
This folder Contains all data and scripts needed to replicate the plots presented in Dennis et al 2017.
FOLDERS AND THEIR CONTENTS:
Fig3_ADLimaging
Dennis2017_imaginganalysis.pdf output of Dennis2017_imaginganalysis.Rmd
Dennis2017_imaginganalysis.Rmd makes all plots and statistics for ADL imaging data used in the manuscript including a separate control experiment completed to demonstrate that ethanol solvent alone cannot explain the responses to C9 nor DEET.
Dennis2017_plot-rawdata.pdf output of Dennis2017_plot-rawdata.Rmd
Dennis2017_plot-rawdata.Rmd plots all ImageJ-generated .txt files (before bleach-correct or deltaF/Fmax calculation).
c9adl Contains individual ImageJ-generated files reflecting fluorescence changes in a single ADL neuron over the course of a single experiment on a single wild type animal given pulses of 100nM C9 (in 0.15% ethanol) at 30-50s, 70-90s, and 110-130s
c9mut Contains individual ImageJ-generated files reflecting fluorescence changes in a single ADL neuron over the course of a single experiment on a single str-217-/- mutant animal given pulses of 100nM C9 (in 0.15% ethanol) at 30-50s, 70-90s, and 110-130s
c9res Contains individual ImageJ-generated files reflecting fluorescence changes in a single ADL neuron over the course of a single experiment on a single str-217-/- mutant animal expressing str-217 under the ADL-specific srh-220 promoter, given pulses of 100nM C9 (in 0.15% ethanol) at 30-50s, 70-90s, and 110-130s
pt0adl Contains individual ImageJ-generated files reflecting fluorescence changes in a single ADL neuron over the course of a single experiment on a single wild type animal given pulses of 0.15% ethanol solvent at 30-50s, 70-90s, and 110-130s
pt0mut Contains individual ImageJ-generated files reflecting fluorescence changes in a single ADL neuron over the course of a single experiment on a single mutant animal given pulses of 0.15% ethanol solvent at 30-50s, 70-90s, and 110-130s
pt0res Contains individual ImageJ-generated files reflecting fluorescence changes in a single ADL neuron over the course of a single experiment on a single str-217-/- mutant animal expressing str-217 under the ADL-specific srh-220 promoter, given pulses of 0.15% ethanol at 30-50s, 70-90s, and 110-130s
pt15adl Contains individual ImageJ-generated files reflecting fluorescence changes in a single ADL neuron over the course of a single experiment on a single wild type animal given pulses of 0.15% DEET (in 0.15% ethanol solvent) at 30-50s, 70-90s, and 110-130s
pt15mut Contains individual ImageJ-generated files reflecting fluorescence changes in a single ADL neuron over the course of a single experiment on a single wild type animal given pulses of 0.15% DEET (in 0.15% ethanol solvent) at 30-50s, 70-90s, and 110-130s
pt15res Contains individual ImageJ-generated files reflecting fluorescence changes in a single ADL neuron over the course of a single experiment on a single wild type animal given pulses of 0.15% DEET (in 0.15% ethanol solvent) at 30-50s, 70-90s, and 110-130s
smoothed_dfoverfmax
Contains a .csv file for each genotype/treatment combination. Each file Contains MATLAB-generated deltaF/Fmax values for each animal. These files are used by Dennis2017_imaginganalysis.Rmd
ImageJ_scripts
Contains two macros used to trim original tiff stacks (remove light pre-exposure) and to track neurons and calculate fluorescence changes over time.
MATLAB_scripts
Contains all MATLAB scripts used to analyze ImageJ-generated txt files and generate bleach-corrected deltaF/Fmax values. The ‘master’ script is GCaMP_ADL and requires the rest of the scripts to run properly.
Fig3_Cell-identification performed by Xin Jin
mutantstr-217_w1_L4_lv50ms.zvi Contains the .zvi file used to generate the composite image in Figure 3a
Fig4_Tracking-and-Optogenetics Contains all .csv files needed to plot all tracking and optogenetics pausing behavior data in Figure 4
figure4_reachr.pdf Output of figure4_reachr.Rmd
figure4_reachr.Rmd Plots all ontogenetic data and statistics
figure4_tracking.pdf Output of figure4_tracking.Rmd
figure4_tracking.Rmd Plots all tracking data and statistics
Figs1-3_Behavior
Dennis_DEETandCelegans_behaviordata.csv Actual data needed for plotting
elegans_output.pdf Output of the .Rmd script
elegans_output.Rmd R markdown script
SuppFig1_AWCimaging performed by May Dobosiewicz
AWC_response_mags All response magnitudes used by .Rmd file, originally generated by the MATLAB script
N2_forplot Smoothed frame-by-frame values for plotting traces
str217_forplot Smoothed frame-by-frame values for plotting traces
AWC_response_mags_rawdata
All files used by MATLAB script in one xlsx file
AWC_N2vSTR217_20161228_MATLABscript.txt
Contains MATLAB script used to generate response magnitudes
responsemags.pdf Output of responsemags.Rmd
responsemags.Rmd Plots all response magnitudes and smoothed traces
SuppFig1_HEKimaging performed by Laura Duvall
hek_data.csv Data used by .Rmd file, from the HEK mis-expression experiments
Dennis2017_HEK_protocol.pdf Detailed protocol used to generate these data
hek_analysis_output.pdf Output of hek_analysis_output.Rmd
hek_analysis_output.Rmd Plots HEK mis-expression data
OTHER FILES:
Dennis2017_master.xlsx
Contains all data necessary for plotting in a multi-sheet excel file
Strains.xlsx
Contains all strain data for any C. elegans strains generated for or used in this manuscript.
Strains.PDF
Contains all strain data for any C. elegans strains generated for or used in this manuscript.
README.txt
Notes:
All R scripts were tested and run in RStudio, using R version 3.3.1 (2016-10-31), Sincere Pumpkin Patch on a x86_64-apple-darwin13.4.0
All MATLAB scripts were tested and run on Matlab version 2014b. Additional scripts for analysis of tracking information can be found in Cho et al. “Parallel encoding of sensory history and behavioral preference during Caenorhabditis elegans olfactory learning” eLife 2016. doi: 10.7554/eLife.14000
All ImageJ scripts were tested and run with ImageJ 1.48v, Java 1.6.0_65 (32-bit)