Biozentrum University of Basel

Spatiotemporal transcriptomes during multicellular development of bacterial swarms reveal supra-generational cooperation

Hannah Jeckel1, 2, *, Kazuki Nosho1, *, Konstantin Neuhaus1, Alasdair D. Hastewell3, Dominic J. Skinner4, Dibya Saha1, Niklas Netter1, Nicole Paczia5, Jörn Dunkel3, and Knut Drescher1

1 Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
2Department of Physics, Philipps-Universität Marburg, Renthof 6, 35032 Marburg, Germany
3Department of Mathematics, Massachusetts Institute of Technology, 02139 Cambridge, MA, USA
4NSF-Simons Center for Quantiative Biology, Northwestern University, IL 60208, USA
5Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043 Marburg, Germany
*equal contribution

Gene expression heatmap explorer

In this heatmap explorer, you can view all gene expression patterns and swarm properties in space and time. The following files are available for download:

Normalized log2 read counts, dynamic range, spatiotemporal score and rank of genes

Sample description

Sequence reads were mapped to the reference chromosomal genome (NZ_CP020102) and its associated natural plasmid pBS32 (NZ_CP020103). Reads mapped to functional genes (CDS, ncRNA, tmRNA, signal recognition particle RNA, and ribonuclease P RNA) were normalized and are displayed below. Raw sequence data and processed data can be downloaded from the GEO database (Accession number: GSE224332). As a main gene name, the corresponding gene name in SubtiWiki v.4 is displayed together with synonyms when applicable, otherwise the gene name according to the annotations of the reference genomes (NZ_CP020102 and NZ_CP020103) is used. The locus tag is also displayed as a unique identifier for genes.

Search/Filter Gene list

Use the input field to search for a specific gene or swarm property. Up to five genes can be displayed at a time. Remove genes by pressing the "x" next to their name featured below.

Gene 1 Gene 2 Gene 3 Gene 4 Gene 5