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Series GSE90743 Query DataSets for GSE90743
Status Public on Mar 27, 2017
Title RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)
Organism Escherichia coli
Experiment type Expression profiling by high throughput sequencing
Summary In large-scale production processes, metabolic control is typically achieved by limited supply of essential nutrients like glucose or ammonia. With increasing bioreactor dimensions, microbial producers such as Escherichia coli are exposed to changing substrate availabilities due to limited mixing. In turn, cells sense and respond to these dynamic conditions leading to frequent activation of their regulatory programs. Previously, we characterized short- and long-term strategies of cells to adapt to glucose fluctuations. Here, we focused on fluctuating ammonia supply, while studying a continuously running two-compartment bioreactor system comprising a stirred tank reactor (STR) and a plug flow reactor (PFR). Genes were repeatedly switched on/off when E. coli returned to the STR. Moreover, E. coli revealed highly diverging long-term transcriptional responses in ammonia compared to glucose fluctuations. The identification of target genes may help to create robust cells and processes for large-scale application.
 
Overall design mRNA time profiles of E. coli K12 W3110 ammonia-limited chemostat STR-PFR culture: 59 samples derived from STR or different PFR sample ports over process time including three samples derived from the reference steady state before PFR addition, in duplicate, generated using Illumina HiSeq 2500.
 
Contributor(s) Simen JD, Löffler M, Matthes J, Jäger G, Schäferhoff K, Takors R
Citation(s) 28447391, 28702020
Submission date Dec 01, 2016
Last update date Jul 01, 2019
Contact name Joana Danica Simen
E-mail(s) joana.simen@ibvt.uni-stuttgart.de
Organization name University of Stuttgart
Department Institute of Biochemical Engineering
Street address Allmandring 31
City Stuttgart
ZIP/Postal code 70569
Country Germany
 
Platforms (1)
GPL18133 Illumina HiSeq 2500 (Escherichia coli)
Samples (59)
GSM2411669 chemostat STR-PFR culture STR 5min, rep1
GSM2411670 chemostat STR-PFR culture STR 10min, rep1
GSM2411671 chemostat STR-PFR culture STR 25min, rep1
Relations
BioProject PRJNA356064
SRA SRP094492

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE90743_E14R025_raw_counts.txt.gz 435.0 Kb (ftp)(http) TXT
GSE90743_E14R025_raw_counts_filtered.txt.gz 406.7 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record
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