Mountain View
biomedical and healthCAre Data Discovery Index Ecosystem
help Advanced Search
Title: RNA-seq system comparison of Streptomyces lividans TK24 cultivated under micro-scale biolector and reference bioreactor conditions      
dateReleased:
08-31-2016
description:
The comprehensive transcriptome of Streptomyces lividans TK24 in a biolector milliliter-scale cultivation system was compared in detail against an established 1000-fold larger lab-scale bioreactor system. For main-cultures, the modified minimal medium NMMP (D'Huys et al. 2011) was applied, containing 2.07 g/L NaH2PO4 x 1 H2O, 2.6 g/L K2HPO4, 0.6 MgSO4 x 7 H2O, 3.0 g/L (NH4)2SO4, 10 g/L D-glucose and 5 g/L BactoTM Casamino acids as well as several trace elements (1 mg/L ZnSO4 x 7 H2O, 1 mg/L FeSO4 x 7 H2O, 1 mg/L MnCl2 x 4 H2O, 1 mg/L CaCl2). pH was adjusted to 6.8 using 1 M KOH or 1 M H2SO4. In all MTP BioLector (BL) cultivations and in some bioreactor experiments (when indicated) 100 mM 2-(N-morpholino)ethanesulfonic acid (MES) was added as biological inert buffer system. Except for the phosphate buffer, all other components were prepared as stock solutions and sterilized separately. For MTP based cultivations the BL device, all stock solutions kept frozen at -20 C in aliquots sufficient for 50 mL final medium, to ensure identical conditions between experimental runs. For the system comparison experiments the same medium charge was used for all cultivations. 1 mL MTP-based BL cultivations MTP cultivations were performed in 48 well FlowerPlates (m2p-labs GmbH, Baesweiler, Germany), covered by a gas-permeable sealing foil (m2p-labs GmbH, Baesweiler, Germany). 1000 L cultivation medium was inoculated to a final OD600 of 0.2. Temperature and humidity was controlled in the incubation chamber of the BL device at 30 C and 89 % respectively. All signals (BS, DO, and pH), were measured with a cycle time of around 10 min. Altogether, 96 identical parallel milliliter-scale cultivations were performed in two separate but identical BL devices. One of these devices was additionally embedded in a lab-robotic liquid handling unit in the style of (Unthan et al. 2015; Rohe et al. 2012), to provide automated hourly sampling for substrate and cell dry weight analysis. The cultivations in the second BL unit served to generate samples for the omics-based analysis, discussed in the later sections. Bioreactor cultivations were carried out in a 1.5 L lab-scale system (DasGip, Jlich, Germany), equipped with two six blade, 46 mm Rushton turbines as well as sensors for DO (Hamilton, Visiferm DO 225) and pH (MettlerToledo, 405-DPAS-SC-K8S/225/120). Temperature was controlled at 30 C; evaporation was minimized by offgas cooling at 10 C. 700 mL phosphate buffer was sterilized directly within the reactor glass vessel; all other media components were added sterile and premixed subsequently by using a 500 mL feeding flask. 0.5 mL anti-foam (AF204 (Sigma, MO, USA)) was added before DO calibration. The final 1000 mL medium was inoculated with washed mycelium to a final OD600 of 0.2. Both, aeration and agitation were set to fixed values at 0.5 vvm and 800 rpm respectively. For both techniques samples were taken during the late growth phase, two hours after the switch to process phase II.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-MTAB-5047
refinement:
raw
dateSubmitted:
04-01-2016
keywords:
functional genomics
dateModified:
08-19-2016
creators:
Tobias Busche
availability:
available
types:
gene expression
name:
Streptomyces lividans
name:
growth condition design
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-5047/E-MTAB-5047.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-5047/E-MTAB-5047.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

Feedback?

If you are having problems using our tools, or if you would just like to send us some feedback, please post your questions on GitHub.