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Data and code for Simon et al (2020) Developmental Cell

UID: 11364

Author(s): Hadjantonakis, Anna-Katerina*, Simon, Claire S.* * MSK affiliated

Description
Description from GitHub:

"Included in this repository are:

1. CellProfiler pipelines for the segmentation and measurement of cytoplasmic and nuclear fluorescence intensities of ERK-KTR-mClover in confocal time-lapse images of hemizygousÊHprtERK-KTRÊand homozygousÊR26NLS-mKate2Êembryos during pre-implantation development. Pipeline A was used by default and Pipeline B and C were used for cells where segmentation was challenging.
CellProfiler/EmbryoPipeline_A.cppipe
CellProfiler/EmbryoPipeline_B.cppipe
CellProfiler/EmbryoPipeline_C.cppipe

2. Matlab script to calculate and output images of the ERK-KTR cytoplasmic : nuclear (C:N) ratio using the CellProfiler outputs.
Matlab/CN_Ratio_mean.m

3. Data of ERK-KTR C:N values from tracked cells in Imaris in Control, MEKi and FGF treated embryos and untreated embryos that were fixed and immunostained to determine end-point lineage identities.
R_and_data/FGF.csv
R_and_data/PD03.csv
R_and_data/Lineage_2hr.csv
R_and_data/Lineage_12hr.csv

4. R scripts for the analysis of the cell tracking data and ERK-KTR C:N used to plot figures and perform statistical tests.
R_and_data/FGF_Analysis.R
R_and_data/MEKi_Analysis.R
R_and_data/Lineage_2hr_Analysis.R
R_and_data/Lineage_12hr_Analysis.R

5. R and Matlab scripts used for setting ERK activity threshold and to plot figures for 2 hour movies.
Matlab/Threshold_finder.m
R_and_data/FGF_Threshold.R
R_and_data/MEKi_Threshold.R
R_and_data/Lineage_2hr_Threshold.R

6. R and Matlab scripts for identifying peaks, plot figures and perform statistical tests for 2 hour movies.
Matlab/PeakCall_smooth_FGF.m
Matlab/PeakCall_smooth_PD03.m
Matlab/PeakCall_smooth.m
R_and_data/FGF_Peak_Analysis.R
R_and_data/MEKi_Peak_Analysis.R
R_and_data/Lineage_2hr_Analysis.R

These scripts were compiled in CellProfiler 2.1 (Lamprecht, et al., 2007), Matlab R2019a, R Studio 1.0.143, and R version 3.5.2 "
Subject(s)
Algorithms
Cytoplasm
Microscopy, Confocal
Software
Time-Lapse Imaging
Access via GitHub

Access Restrictions
Free to All
Access Instructions
Accessible via GitHub
DOI
10.1016/j.devcel.2020.09.030
Associated Publications
Simon C, Rahman S, Raina D, Schröter C, Hadjantonakis A. Live visualization of ERK activity in the mouse blastocyst reveals lineage-specific signaling dynamics. Developmental Cell. 2020; 55(3):341-353.e5.
Software Used
CellProfiler

Free open-source software for measuring and analyzing cell images.

MATLAB

a programming and numeric computing platform

R

a free software environment for statistical computing and graphics.

Dataset Format(s)
R, CSV, M, CPPIPE
Data Catalog Record Updated
2024-09-16