Data files

The pdf-file shows simulations of a hypothetical model of sigma factor competition. It simulates the dynamics that we can expect from the experiments and prepares for the analysis of the experimental data. Analysis of sigma factor competition is based on a Lineweaver-Burk representation of RNApolymerase and competing sigma factors.

B. subtilis was grown in minimal media in a chemostat at different growth rates (µ= max, µ=0.1, µ=0.4) and in the presence of 1.2M NaCl (µ=0.1) with or without glycinebetaine. Here you'll find cell titers for every sample.

B. subtilis was grown in minimal media in a chemostat at different growth rates (µ= max, µ=0.1, µ=0.4) and in the presence of 1.2M NaCl (µ=0.1) with or without glycinebetaine. Here you'll find cell sizes for every sample.

B. subtilis was grown in minimal media in a chemostat at growth rate µ=0.1, with 1.2M NaCl, without glycine betaine. Relative quantification for the proteome was done using metabolic labeling.

B. subtilis was grown in minimal media in a chemostat at growth rate µ=0.1, with 1.2M NaCl and glycine betaine. Relative quantification for the proteome was done using metabolic labeling.

Batch sample publishing

Batch sample publishing

batch fermatation - The transition from growing to non-growing Bacillus subtilis cells

Array hybridisation was done at Roche Nimblegen Inc. It cannot be displayed over here.

batch fermatation - The transition from growing to non-growing Bacillus subtilis cells

This code uses the PEtab problem (written in the yaml file) to perform MCMC sampling with pyPESTO. Afterwards an ensemble is created, that allows to compute the posterior predictive distribution and therefore the credibility intervals for the model output.

The sampling.py scipt of pyPESTO visulize was adjusted for an improved visualization. The used code was also uploaded.

A Conda environment file (.yml) containing the specific version of Python and installed packages with the according versions, ...

BCN-RNAsample001

BCN-RNAsample002

BCN-RNAsample003

BCN-RNAsample004

BCN-RNAsample005

BCN-RNAsample006

BCN-RNAsample007

BCN-RNAsample008

BCN-RNAsample009

BCN-RNAsample010

BCN-RNAsample011

BCN-RNAsample012

BCN-RNAsample013

BCN-RNAsample014

BCN-RNAsample015

BCN-RNAsample016

BCN-RNAsample017

BCN-RNAsample018

BCN-RNAsample019

BCN-RNAsample020

BCN-RNAsample021

BCN-RNAsample022

BCN-RNAsample023

BCN-RNAsample024

BCN-RNAsample025

BCN-RNAsample026

BCN-RNAsample027

BCN-RNAsample028

BCN-RNAsample029

BCN-RNAsample030

BCN-RNAsample031

BCN-RNAsample032

BCN-RNAsample033

BCN-RNAsample034

BCN-RNAsample035

BCN-RNAsample036

Previously identified gene targets were used as input (see miRNA gene target file).

Literature-curated transcription factor (TF) - miRNA pairs of deregulated miRNAs were extracted from TransmiR (Tong, Cui and Wang 2019 TransmiR). miRNA, target gene, and TF Interaction pairs were visualized in Cytoscape v3.8.2 (Shannon, P. et al. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research 13, 2498-2504, doi:Doi 10.1101/Gr.1239303 (2003). The missing ...

Previously identified gene targets were used as input (see miRNA gene target file).

Literature-curated transcription factor (TF) - miRNA pairs of deregulated miRNAs were extracted from TransmiR (Tong, Cui and Wang 2019 TransmiR). miRNA, target gene, and TF Interaction pairs were visualized in Cytoscape v3.8.2 (Shannon, P. et al. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research 13, 2498-2504, doi:Doi 10.1101/Gr.1239303 (2003). The missing ...

BC7 NLM-Chem-track data and materials

Microscopy images of A.Caldus (A), L.ferriphilum (L), S.thermosulfidooxidans (S) biofilms on chalcopyrite particles. (individual,e.g. SXX or mixed, e.g. SAL, cultures)

Timepoints: Day1, Day3, Day7, Day14, Day21

Data for Figs. 5D, 5E and Supp 7C in Chew et al. PNAS 2014 FW - fresh weight DW - dry weight (i.e. after baking out all water) SLA - specific leaf area (area per g mass), indicates leaf thickness Indiv, data for individual leaves rather than rosette

Excel sheet with mean and SD biomass data and charts, individual metabolite replicates, mean, SD and charts Details on Read.ME worksheet

Protein, RNA and DNA content during the logarithmic growth phase were investigated in this study. The values represent the average of at least three independent experiments. Errors represent the standard deviation between the experiments.

Data for Figs. 2I, 2J, 2K in Chew et al. PNAS 2014 Fresh biomass, dry biomass (i.e. after baking out all water), SLA - specific leaf area (area per g)

The same data are available on the BioDare resource, with additional experimental meta data on growth conditions. BioDare ID 13790828881028, title "Physiology experiment using Col", the direct link is: https://www.biodare.ed.ac.uk/robust/ShowExperiment.action?experimentId=13790828881028

Data for Figs. 3D, 3E in Chew et al. PNAS 2014 Fresh biomass, dry biomass (i.e. after baking out all water), SLA - specific leaf area (area per g) Also FMv1 model simulation results.

The same data are available on the BioDare resource, with additional experimental meta data on growth conditions. BioDare ID 13790837647786, title "Physiology experiment using Fei", the direct link is: https://www.biodare.ed.ac.uk/robust/ShowExperiment.action?experimentId=13790837647786

Data for Figs. 3A, 3B in Chew et al. PNAS 2014 Fresh biomass, dry biomass (i.e. after baking out all water), SLA - specific leaf area (area per g)

Also contains model simulation data from the FMv1 The same data are available, with additional experimental meta data on growth conditions, from the BioDare resource: BioDare experiment 13790834110003; title "Physiology experiment using Ler", the direct link is: https://www.biodare.ed.ac.uk/robust/ShowExperiment.action?experimentId=13790834110003

Biomass weight during glucose pulse. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines, etc) were measured.

Data file for PLaSMo accesssion ID PLM_8, version 1

• MNT-021_J-20-0152_Bl6J_CYP1A2-1/500_Run 08_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_002 > Control
• MNT-022_J-20-0154_Bl6J_CYP1A2-1/500_Run 08_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_002 > Control
• MNT-023_J-20-0156_Bl6J_CYP1A2-1/500_Run 08_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_002 > Control
• MNT-024_J-20-0158_Bl6J_CYP1A2-1/500_Run 08_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_002 > Control
• MNT-025_J-20-0160_Bl6J_CYP1A2-1/500_Run ...

• MNT-021_J-20-0152_Bl6J_CYP1A2-1/500_Run 08_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_002 > Control
• MNT-022_J-20-0154_Bl6J_CYP1A2-1/500_Run 08_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_002 > Control
• MNT-023_J-20-0156_Bl6J_CYP1A2-1/500_Run 08_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_002 > Control
• MNT-024_J-20-0158_Bl6J_CYP1A2-1/500_Run 08_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_002 > Control
• MNT-025_J-20-0160_Bl6J_CYP1A2-1/500_Run ...

• MNT-021_Bl6J_J-20-0152_CYP2E1- 1/400_Run 011_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_006 >Control
• MNT-022_Bl6J_J-20-0154_CYP2E1- 1/400_Run 011_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_006 >Control
• MNT-023_Bl6J_J-20-0156_CYP2E1- 1/400_Run 011_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_006 >Control
• MNT-024_Bl6J_J-20-0158_CYP2E1- 1/400_Run 011_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_006 >Control
• MNT-025_Bl6J_J-20-0160_CYP2E1- 1/400_Run ...

• MNT-021_Bl6J_J-20-0152_CYP2E1- 1/400_Run 011_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_006 >Control
• MNT-022_Bl6J_J-20-0154_CYP2E1- 1/400_Run 011_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_006 >Control
• MNT-023_Bl6J_J-20-0156_CYP2E1- 1/400_Run 011_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_006 >Control
• MNT-024_Bl6J_J-20-0158_CYP2E1- 1/400_Run 011_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_006 >Control
• MNT-025_Bl6J_J-20-0160_CYP2E1- 1/400_Run ...

• MNT-021_J-20-0152_CYP3A4 1/2000_Run 10_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_005 > Control
• MNT-022_J-20-0154_CYP3A4 1/2000_Run 10_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_005 > Control
• MNT-023_J-20-0156_CYP3A4 1/2000_Run 10_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_005 > Control
• MNT-024_J-20-0158_CYP3A4 1/2000_Run 10_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_005 > Control
• MNT-025_J-20-0160_CYP3A4 1/2000_Run 10_LLL(green), RML(red), ...

• MNT-021_J-20-0152_HE_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_003 > Control
• MNT-022_J-20-0154_HE_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_003 > Control
• MNT-023_J-20-0156_HE_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_003 > Control
• MNT-024_J-20-0158_HE_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_003 > Control
• MNT-025_J-20-0160_HE_LLL(green), RML(red), RSL (black), ICL(yellow)_MAA_003 > Control
• MNT-026_J-20-0162_HE_LLL(green), RML(red), ...