Study Description: 
The data presented here is an original dataset of the raw data underlying the figures in the publication "Epigenetic small molecule screening identifies a new HDACi compound for ameliorating Duchenne muscular dystrophy." In this publication, we used an established animal model for DMD, the zebrafish strain sapje, to screen a library of >800 epigenetic small molecules. We found that a single early treatment of the HDACi SR-4370 can ameliorate the muscle phenotype, increase lifespan in dmd zebrafish, and increase histone acetylation. These results support the effectiveness of small molecule screening in DMD zebrafish and add to the growing evidence of HDACi as promising candidates for treating DMD. The data was generated using the methods described in the resulting publication.

Research Domain: Biological sciences

Keywords: Duchenne muscular dystrophy, epigenetic therapy, HDAC inhibitor, zebrafish, drug screen

Funding Information: This work was supported by the National Institutes of Health 5R01AR076978 and National Institutes of Health grant 5R90DE023059. The funding sources had no involvement in the conduct of the research or preparation of the article.

Data and File Overview

Each file in this folder contains the raw data generated for this study.

List of Tables and Files provided:

 table_1_qualitative_phenotypic_data.csv

This table provides the raw data underlying the graphs shown in Fig. 1D, S1, 2A-B, and S2. Due to the number of treatments and animals needed, the experimental batch is included as column 1. Treatment, concentration, duration, library plate, row, and column location are indicated in columns 2-7. Numeric suffix on columns 8-27 indicates the biological replicate (i.e., 1-4) from which the data were obtained. "Dead" indicates generalized lethality within the corresponding biological replicate and exposure conditions. "Standard" indicates treatment from 24-96 hours post-fertilization (hpf) as described in the methods and illustrated in Fig. 4B. WT, wild type. DMSO, dimethyl sulfoxide.

 table_2_library_compounds.csv

This table lists all included compounds and their corresponding plate number and well locations (row/column format) in the screening library (MedChemExpress, Monmouth Junction, NJ; Catalog #HY-L005).

 table_3_pool_model.csv

This table lists pre-processed data underlying the graph shown inFig.2A. Data in this file was derived from and summarizes data in “table_1_qualitative_phenotypic_data.csv”. This file was subsequently run using the provided code (see CODE/SOFTWARE). WT, wild type. DMSO, dimethyl sulfoxide.

 table_4_qbiref_initial.csv

This table provides the raw data underlying graph 2D. Data shown are the raw mean gray values used in the quantitative birefringence analysis of wild type (WT) or mutant dmd larvae treated with the indicated compounds and concentrations. Column 1 labeled "plate/well" refers to locations on 12-well testing plates and was used to identify and organize data into biological replicates. DMSO, dimethyl sulfoxide.

 table_5_qbiref_compare_vendor.csv

This table provides the raw data underlying graph 3A. Data shown are the raw mean gray values used in the quantitative birefringence analysis of wild type (WT) or mutant dmd larvae treated with the indicated compounds and concentrations. Column 1 labeled "plate/well" refers to locations on 12-well testing plates and was used to identify and organize data into biological replicates. DMSO, dimethyl sulfoxide.

 table_6_qbiref_external_validation.csv

This table provides additional raw data underlying graph 3B. Data shown are the raw mean gray values used in the quantitative birefringence analysis of wild type (WT) or mutant dmd larvae treated with the indicated compounds and concentrations. These values (recorded at the University of Maine) were compared to data in “table_4_qbiref_initial.csv”, also shown in 2D.  DMSO, dimethyl sulfoxide.

 table_7_qbiref_SR_low.csv

This table provides the raw data underlying graph 4A. Data shown are the raw mean gray values used in the quantitative birefringence analysis of wild type (WT) or mutant dmd larvae treated with the indicated compounds and concentrations. Column 1 labeled "plate/well" refers to locations on 12-well testing plates and was used to identify and organize data into biological replicates. DMSO, dimethyl sulfoxide.

 table_8_qbiref_SR_high.csv

This table provides the raw data underlying graph 4A. Data shown are the raw mean gray values used in the quantitative birefringence analysis of wild type (WT) or mutant dmd larvae treated with the indicated compounds and concentrations. Column 1 labeled "plate/well" refers to locations on 12-well testing plates and was used to identify and organize data into biological replicates. DMSO, dimethyl sulfoxide.

 table_9_qbiref_SR_times.csv

This table provides the raw data underlying graph 4C. Data shown are the raw mean gray values used in the quantitative birefringence analysis of wild type (WT) or mutant dmd larvae treated with the indicated compounds, concentrations, and from the indicated time in hours post-fertilization (hpf). Column 1 labeled "plate/well" refers to locations on 12-well testing plates and was used to identify and organize data into biological replicates. DMSO, dimethyl sulfoxide.

 table_10_myotomes.csv

This table provides the raw data underlying graph 4G. Data shown are the raw counts of affected/lesioned or unaffected/normal myotomes in wild-type (WT) or mutant dmd larvae treated with the indicated compounds and concentrations. DMSO, dimethyl sulfoxide.

 table_11_qbiref_ox_row.csv

This table provides the raw data underlying graph 5A. Data shown are the raw mean gray values used in the quantitative birefringence analysis of wild type (WT) or mutant dmd larvae treated with the indicated compounds and concentrations. Column 1 labeled "plate/well" refers to locations on 12-well testing plates and was used to identify and organize data into biological replicates. DMSO, dimethyl sulfoxide.

 table_12_qbiref_ox_col.csv

This table provides the raw data underlying graph 5A. Data shown are the raw mean gray values used in the quantitative birefringence analysis of wild type (WT) or mutant dmd larvae treated with the indicated compounds and concentrations. Column 1 labeled "plate/well" refers to locations on 12-well testing plates and was used to identify and organize data into biological replicates. DMSO, dimethyl sulfoxide.

 table_13_qbiref_ox_indiv.csv

This table provides the raw data underlying graph 5B. Data shown are the raw mean gray values used in the quantitative birefringence analysis of wild type (WT) or mutant dmd larvae treated with the indicated compounds and concentrations. Column 1 labeled "plate/well" refers to locations on 12-well testing plates and was used to identify and organize data into biological replicates. DMSO, dimethyl sulfoxide.

 table_14_qbiref_ox_elim.csv

This table provides the raw data underlying graph 5C. Data shown are the raw mean gray values used in the quantitative birefringence analysis of wild type (WT) or mutant dmd larvae treated with the indicated compounds and concentrations. Column 1 labeled "plate/well" refers to locations on 12-well testing plates and was used to identify and organize data into biological replicates. DMSO, dimethyl sulfoxide.

 table_15_qbiref_ox_pairwise.csv

This table provides the raw data underlying graph 5D. Data shown are the raw mean gray values used in the quantitative birefringence analysis of wild type (WT) or mutant dmd larvae treated with the indicated compounds and concentrations. Column 1 labeled "plate/well" refers to locations on 12-well testing plates and was used to identify and organize data into biological replicates. DMSO, dimethyl sulfoxide.

 table_16_qbiref_hdaci.csv

This table provides the raw data underlying graph 6A. Data shown are the raw mean gray values used in the quantitative birefringence analysis of wild type (WT) or mutant dmd larvae treated with the indicated compounds and concentrations. Column 1 labeled "plate/well" refers to locations on 12-well testing plates and was used to identify and organize data into biological replicates. DMSO, dimethyl sulfoxide.

 table_17_qbiref_hdaci_add.csv

This table provides the raw data underlying graph 6A. Data shown are the raw mean gray values used in the quantitative birefringence analysis of wild type (WT) or mutant dmd larvae treated with the indicated compounds and concentrations. Column 1 labeled "plate/well" refers to locations on 12-well testing plates and was used to identify and organize data into biological replicates. DMSO, dimethyl sulfoxide.

 table_18_western_hdaci.csv

This table provides the raw data underlying graphs 6D-F. Data shown are the raw band intensities in Western analysis of wild type (WT) or mutant dmd larvae treated with the indicated compounds and concentrations. Column "gel" refers to the gel image (as shown in Supplemental Figure S3) from which measurements were obtained. DMSO, dimethyl sulfoxide.

 table_19_survival.csv

This table provides the raw data underlying graph 7A. The data shown are the raw counts of surviving larvae treated with the indicated compounds. Column "dpf" indicates the day post-fertilization at which animals were counted. Column names specify compound, replicate, and lesion status (i.e., AFFECTED or unaffected) of each recorded tank. WT, wild type. DMSO, dimethyl sulfoxide.

 table_20_survival_multiple.csv

This table provides the raw data underlying graph 7B. The data shown are the raw counts of surviving larvae treated with the indicated compounds. Column "dpf" indicates the day post-fertilization at which animals were counted. Column names specify compound, replicate, and lesion status (i.e., AFFECTED or unaffected) of each recorded tank. WT, wild type. DMSO, dimethyl sulfoxide.

regression_analysis.txt

This file contains the R script used to generate data underlying the graph shown in Fig. 2A. Data format from “table_3_pool_model.csv” should be retained, and code should be executed in order. Default settings were used for analysis.

Code/Software

Regression analysis was run in R v4.4.1 using the package GLM v14. Analysis also requires the tidyverse package to be loaded in the environment. Raw data for replicates in file "table_1_qualitative_phenotypic_data.csv" were aggregated and simplified to generate the starting file "table_3_pool_model.csv". To recreate the analysis, data should be kept in the same format, and the code in “regression_analysis.txt” should be executed in order.