Genoscapist

Reference genome

Bacillus subtilis subsp. subtilis strain NDmed, whole genome shotgun sequence (10 contigs)

Associated publication

This Genoscapist website presents graphical representation of data from the following publication:

Direct comparison of spatial transcriptional heterogeneity across diverse Bacillus subtilis biofilm communities.
Yasmine Dergham, Dominique Le Coq, Pierre Nicolas, Elena Bidnenko, Sandra Dérozier, Maxime Deforet, Eugénie Huillet, Pilar Sanchez-Vizuete, Julien Deschamps, Kassem Hamze, Romain Briandet.
Nature Communications 14, 7546 (2023).  doi.org/10.1038/s41467-023-43386-w

Dedicated method for RNA-seq coverage representation have been developed specifically for this study and have been described in the above publication.

Associated GEO records

Link	Description
GSE214964	From shaken planktonic cultures, the exponential (EX) and the stationary (ST) phase were collected. The stationary phase cultures were used to inoculate static liquid cultures and semi-solid agar plates, which were incubated for 24 hours. From the static liquid culture, three localized compartments were collected separately: the pellicle (PL) formed at the air-liquid interface, the submerged biofilm (SB) formed on the solid-liquid interface, and the free detached cells (DC) between these two compartments were collected separately. From the semi-solid agar plate, four localized compartments were collected separately: the mother colony (MC), corresponding to the inoculation site from which the swarm has developed as a mature macrocolony; the base (BS) of the dendrites in the early biofilm form; the dendrites (DT), a monolayer of cells ready to form later the biofilm; and the tips (TP) formed of motile and highly dividing cells. the base (BS) of the dendrites in the early biofilm form; the dendrites (DT), a monolayer of cells ready to form later the biofilm; and the tips (TP) formed of motile and highly dividing cells. For each compartment, three independent samples were taken as biological replicates and subjected to transcriptome analysis (RNA-Seq).

Link

Description

GSE214964

From shaken planktonic cultures, the exponential (EX) and the stationary (ST) phase were collected. The stationary phase cultures were used to inoculate static liquid cultures and semi-solid agar plates, which were incubated for 24 hours. From the static liquid culture, three localized compartments were collected separately: the pellicle (PL) formed at the air-liquid interface, the submerged biofilm (SB) formed on the solid-liquid interface, and the free detached cells (DC) between these two compartments were collected separately. From the semi-solid agar plate, four localized compartments were collected separately: the mother colony (MC), corresponding to the inoculation site from which the swarm has developed as a mature macrocolony; the base (BS) of the dendrites in the early biofilm form; the dendrites (DT), a monolayer of cells ready to form later the biofilm; and the tips (TP) formed of motile and highly dividing cells. the base (BS) of the dendrites in the early biofilm form; the dendrites (DT), a monolayer of cells ready to form later the biofilm; and the tips (TP) formed of motile and highly dividing cells. For each compartment, three independent samples were taken as biological replicates and subjected to transcriptome analysis (RNA-Seq).

Initial Genoscapist publication

Nicolas P, Mäder U, Dervyn E, et al. Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis.
Science. 2012;335(6072):1103-1106.  doi:10.1126/science.1206848  Genoscapist website  Demonstration