Quantitative Data and Analyses for Vincent, et al. 2018

This fileset includes raw data and code for the analyses contained in Vincent, et al. 2018, "Hunchback is counter-repressed to regulate <i>even-skipped</i> stripe 2 expression in Drosophila embryos." In this study, we present evidence that the transcription factor Hunchback directly represses the <i>eve </i>stripe 3+7 enhancer and is counter-repressed in regulation of the <i>eve </i>stripe 2+7 enhancer. We collected quantitative, cellular resolution<i> </i>gene expression data in wild-type and perturbed Drosophila embryos containing reporter constructs for these enhancers. We also examined binding site enrichment in orthologous <i>eve </i>enhancers. Our results alter the canonical description of the <i>eve </i>stripe 2 enhancer where Hunchback is considered a direct activator; Hunchback instead represses this enhancer, and this repression is counteracted by additional sequence features.<br>The following files contain the data and the code used to generate the figures and tables contained in the study. We hope they will prove useful for the community.<br>Vincent2018_MATLAB: This is a compressed file containing raw data and code. This file contains subfiles organized this file by figure or table number, and each subfile contains commented MATLAB code, plots, and raw data in the form of pointclouds, or cellular resolution expression measurements from individual embryos.<br>PWMSforEnhancerMutations: This is a compressed file containing frequency position weight matrices for transcription factors expressed in the embryo. We used these matrices to predict binding sites for these factors with PATSER, a program available from the Stormo lab (http://stormo.wustl.edu/software.html). We generated these matrices from count matrices published in Noyes, et al. 2008 and Schroeder, et al. 2011 using a pseudocount of 1.<br>SitePredictionsforEnhancerMutations: This compressed file contains individual csv files with the binding site predictions used to design <i>eve </i>enhancers with binding site mutations. Each file all predicted binding sites within the enhancer, along with their coordinates and PATSER scores. We used a p-value cutoff of 0.003 to make these predictions.<br>PWMsforEnrichment: This is a compressed file containing frequency position weight matrices for Bicoid, Caudal, Hunchback and Krüppel. We used these matrices to predict binding sites for these factors with PATSER, a program available from the Stormo lab (http://stormo.wustl.edu/software.html). We generated these matrices from count matrices available through FlyFactorSurvey (Zhu, et al. 2011, http://mccb.umassmed.edu/ffs/) using a pseudocount of 0.1.<br>SitePredictionsforEnrichment: This compressed file contains individual csv files with the binding site predictions used to calculate binding site enrichment scores in orthologous <i>eve </i>enhancers (see Hare, et al. 2008 for enhancer sequences, and Wunderlich, et al. 2015 for the computational methods). Each file all predicted binding sites within the enhancer, along with their coordinates and PATSER scores. We used the default PATSER p-value cutoff to make these predictions. Scores for binding sites predicted in all DNAse accessible regions in stage 5 of embryogenesis (Thomas, et al. 2011) can be found in the corresponding folders in Vincent2018_MATLAB.<br>