GEO DataSets

(Submitter supplied) By using transcriptomics, we studied the spatiotemporal transcriptional changes in Escherichia coli biofilm colonies

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26155

48 Samples

Download data: TXT

(Submitter supplied) Gene expression changes during biofilm formation processes were investigated. The gene expression was compared at attachment, colony formation and maturation during biofilm formation. At the same time, the gene expressions were also compared with exponential phase and stationary phase in planktonic cells. The gene expression pattern at attachment and colony formation processes showed similar pattern with those in planktonic exponential phase, and the gene expression pattern at maturation process showed similar pattern with those in planktonic stationary phase. more...

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL199

15 Samples

Download data: CEL, DCP

(Submitter supplied) Spatial transcriptome uncovers rich coordination of metabolism and signaling in bacterial community (data 2)

Organism:

Escherichia coli K-12

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26856

6 Samples

Download data: TXT

(Submitter supplied) We developed a spatially resolved method to profile the spatial transcriptome of biofilm. In detail, we used fluorescent dyes to label the different regions of biofilm cultured in a microfluidic chip. After staining, the bacterial cells in biofilm were sorted into relevant bins according to their spatial information marked by the fluorescent pattern. Finally, miniBac-seq (RNA-seq) method was applied to capture the transcriptome of each bin.

Organism:

Escherichia coli BW25113

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27123

38 Samples

Download data: TXT

(Submitter supplied) Gene expression of (i) K-12 yceP biofilms upon addition of 600 µM indole in LB glu medium, (ii) K-12 biofilms due to the trpE mutation in LB glu medium, and (iii) K-12 biofilms due to the tnaA mutation in LB medium. Keywords: indole effect and cell type comparison

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL199

7 Samples

Download data: CEL, EXP

(Submitter supplied) Previously, we discovered that the global regulator Hha is related to cell death in biofilms and regulates cryptic prophage genes. Here we show Hha induces excision of prophage CP4-57 and DLP12 by inducing excision genes and by reducing SsrA synthesis. SsrA is a tmRNA important for rescuing stalled ribosomes, contains an attachment site for CP4-57, and is shown here to be required for CP4-57 excision. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

2 Samples

Download data: CEL, CHP

(Submitter supplied) We employed the orthogonally detectable red, green, and blue fluorescent proteins in a single vector system, dubbed RGB-S reporter, to enable simultaneous, independent and real-time analysis of the stress response in E. coli to physiological stress, genotoxicity, and cytotoxicity.

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29216

10 Samples

Download data: CSV

(Submitter supplied) Using transcriptomics, we studied the spatiotemporal dynamics of B. subtilis swarming colonies on soft-agar surface and identified functional subpopulations.

Organism:

Bacillus subtilis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30886 GPL29318

317 Samples

Download data: CSV