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| Status |
Public on Jan 05, 2023 |
| Title |
Spatial transcriptome unveils the heterogeneity between subpopulations of Bacillus subtilis surface-associated communities |
| Organism |
Bacillus subtilis |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Bacillus subtilis has been extensively used as a model for molecular studies on biofilm formation.
These studies encompassed the development of complex macro-colonies on agar, the formation of pellicles at the air-liquid interface, and lately the formation of submerged architectural biofilms at the solid-liquid interface.
Beside similarities, these multicellular communities also display considerable heterogeneity at the structural, chemical and biological levels.
Here we use RNA-seq to analyze nine different spatio-physiological conditions, including the three biofilm populations (colony, pellicle, and submerged).
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| Overall design |
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).
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| Contributor(s) |
DERGHAM Y, LE COQ D, NICOLAS P, BRIANDET R |
| Citation(s) |
37985771 |
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| Submission date |
Oct 06, 2022 |
| Last update date |
Dec 08, 2023 |
| Contact name |
Pierre Nicolas |
| E-mail(s) |
pierre.nicolas@inrae.fr
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| Phone |
+33-1-3465-2894
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| Organization name |
INRAE - Université Paris-Saclay
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| Lab |
MaIAGE
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| Street address |
INRAE - Domaine de Vilvert
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| City |
Jouy-en-Josas |
| ZIP/Postal code |
F-78350 |
| Country |
France |
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| Platforms (1) |
| GPL28092 |
NextSeq 550 (Bacillus subtilis) |
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| Samples (27)
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| GSM6619208 |
ST, rep1 |
| GSM6619209 |
ST, rep2 |
| GSM6619210 |
ST, rep3 |
| GSM6619211 |
MC, rep1 |
| GSM6619212 |
MC, rep2 |
| GSM6619213 |
MC, rep3 |
| GSM6619214 |
BS, rep1 |
| GSM6619215 |
BS, rep2 |
| GSM6619216 |
BS, rep3 |
| GSM6619217 |
DT, rep1 |
| GSM6619218 |
DT, rep2 |
| GSM6619219 |
DT, rep3 |
| GSM6619220 |
TP, rep1 |
| GSM6619221 |
TP, rep2 |
| GSM6619222 |
TP, rep3 |
| GSM6619223 |
SB, rep1 |
| GSM6619224 |
SB, rep2 |
| GSM6619225 |
SB, rep3 |
| GSM6619226 |
DC, rep1 |
| GSM6619227 |
DC, rep2 |
| GSM6619228 |
DC, rep3 |
| GSM6619229 |
PL, rep1 |
| GSM6619230 |
PL, rep2 |
| GSM6619231 |
PL, rep3 |
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| Relations |
| BioProject |
PRJNA887802 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE214964_processeddata_bsubbiofilm.csv.gz |
518.1 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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