Resources

Downloads of datasets and software

Gene expression atlases

We gather cellular resolution data on gene expression in Drosophila blastoderm embryos, and convert this data into gene expression atlases where measurements for many genes are present in the same average morphological framework. These data are especially useful for challenging computational models of gene expression.  The methods are described in Luengo Hendriks et al., 2006; Fowlkes et al., 2008; Fowlkes et al., 2011; and Wunderlich et al., 2014, as well as on the website of the Berkeley Drosophila Transcription Network Project, where these methods were developed.

Links to specific datasets are below.

Bicoid RNAi atlas

We used RNAi to knockdown expression of the maternally deposited transcription factor bicoid, and measured the response of 13 genes in the anterior posterior patterning network (Staller et al 2013, Genetics; Staller et al., 2015, Development, in press).Download from Figshare

Eve reporter constructs

As part of our study on gene expression in Bcd RNAi embryos, we also measured expression of a set of even-skipped reporter constructs in wildtype D.melanogaster embryos. That data is described in Staller et al., 2015, Development, in press.

Download from Figshare

D.mel atlas

The wildtype Drosophila melanogaster atlas can be downloaded from the Berkeley Drosophila Transcription Network Project.

D.yak & D.pse atlases

We measured mRNA expression patterns for 13 anterior/posterior patterning genes in Drosophila yakuba and Drosophila pseudoobscura, as described in Fowlkes et al., PLoS Genetics 2011Download the D.yak atlas (v1.0) Download the D.pse atlas (v1.0)

Software

We make use of a variety of custom software for visualizing and analyzing our data. These packages are all freely available as described below.

PointCloudXPlore

PointCloudXPlore is a freely available software package for visualizing BDTNP pointclouds and atlas files, developed by the IDAV at UC Davis in collaboration with the BDTNP. It is described in Rubel et al., 2006.Download PointCloudXplor from BDTNP

PointcloudToolBox

The PointcloudToolBox is a set of MATLAB tools for analyzing pointcloud and atlas files, developed by the BDTNP.Download PointCloudToolbox from BDTNP

Atlas Building Software

To build atlases from Pointclouds, we collaborate with Charless Fowlkes and make use of the PointCloudAlign toolkit, developed while he was at Berkeley.Download Pointcloud Align from BDTNP

MulteeSum

In collaboration with Miriah Meyer, we built MulteeSum, an interactive software package to visualize comparison of cellular gene expression profiles, described in Meyer et al., 2011. You can download the software below, preconfigured to browse the figures from Fowlkes et al., 2011. Usage instructions can be found here.

Download MulteeSum

InSite

Also in collaboration with Miriah, we are currently developing a browser to visualize transcription factor binding sites, a seemingly simple, but visually complicated problem. The first version of the tool can be downloaded below.

Download InSite