SOPs

Detailed description of the methods applied for proteomic analyses of P. cordatum heat stress response

Detailed description of the methods applied for metabolomic analyses of P. cordatum heat stress response

This file contains the script for the downstream scRNA-Seq analysis including quality control using the barcode ranking method together with the tool DropletUtils to exclude empty droplets and undetected genes as well as standard data processing (normalisation, variable feature identification, scaling, and dimensionality reduction) using tools of Seurat (v.3.2.2). After cluster annotation the %mtDNA was plotted for both datasets.

This file contains the detailed experimental protocol for the cultivation of "induced sinoatrial bodies (iSABs), the scRNA-Seq procedure as well as the general computational workflow for data processing. The R-script is provided separately.

This file contains the R-script to analyse single nuclei and single cell data of Bl6 and Fzt:DU mice previously processed with cellranger. The analyses utilizes the Seurat and harmony package to integrate three datasets before subsequent downstream analysis characterizing proliferative cardiomyocytes.

This file contains the detailed experimental protocol to isolate nuclei from murine hearts.

This R-script contains the single nuclei analysis for our Fzt:DU and BL6 data, namely bustools file integration, preprocessing, scaling, clustering, marker indentification and annotation of markers and RNAvelocity computation.

Detection of small RNAs by blot hybridization.

Describes the steps required in order to detect and quantify alcohols and other volatile compounds in microbial culture supernatants by gas chromatography with a flame-ionization detector (GC-FID).

This protocol describes the analysis of RNA-Seq data to identify differential expressed genes between two samples. The protocol is simply the analysis of the data and do not include the sequencing protocol.

Metabolomics perturbation sample preparation and description of how the exact details of the perturbations. Perturbations: -Glucose starvation -Amino acid starvation -Fe2+ depletion -Oxidative stress via H2O2 -Glycerol addition to the medium

Standard Operating Procedure describing the process and software used in generating a Genome Scale Metabolic model of M. hyopneumoniae. Used software: Pathway tools PathLogic Cobrapy the Cobra Toolbox libSBML

Describes the cultivation-, washing- and electroporation-steps required in order to transform bacterial cells with DNA.

Describes the steps required in order to run an error-prone PCR (epPCR) for the creation of DNA libraries of a given template gene.

Oxygen gradients were developed as a quick and easy way to simultaneously adapt (recombinant) strains to decreasing levels of oxygen and monitor their progress over multiple days. This SOP can be used for o/n checks or for adaptation experiments spanning over multiple days. For the latter, a time-lapse camera setup is recommended. This SOP can also be applied to check the oxygen requirements of unknown strains.

Matlab script that reproduces the model redesign results outlined in RobOKoD: microbial strain design for (over)production of target compounds (http://fairdomhub.org/publications/236).

Matlab script that reproduces the model redesign results outlined in RobOKoD: microbial strain design for (over)production of target compounds (http://fairdomhub.org/publications/236) for OptKnock.

Matlab script that reproduces the model redesign results outlined in RobOKoD: microbial strain design for (over)production of target compounds (http://fairdomhub.org/publications/236) for RobustKnock.