SOPs

Instructions and details on the data analysis workflow.

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.

Aceton precipitation and protein digestion for proteomic workflow

SOP for bioleaching experiments carried out for microscopy analysis at UDE

steps conducted to pellet cells for RNA and protein extraction

This file describes the naming system used to uniquely identify samples

SOP for extracting DNA, RNA and Proteins from the mineral pellet of a bioleaching culture using hot acidic phenol.
Current draft.

Protocol for the extraction of biomolecules (DNA,RNA,protein,metabolties) from the same sample. Originally intended for lipid accumulating organisms (LAO) from wastewater treatment plant samples.
So far succesfully used for pelleted cells from planktonic cultures.

sampling procedure for mineral containing leaching experiments

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.

Master Bash script to launch Molecular Dynamics when running the Simulation part of Simulation Foundry.
Make sure you followed "Preparations" instructions!
Read the Manual!

Master Bash script to launch Molecular Dynamics when running the Analysis part of Simulation Foundry.
Make sure you followed "Preparations" instructions!
Read the Manual!

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

We have adapted the definitions of terms in [ISA best practice][1] and [programmes and projects][2]:

Programme = Overarching research theme (The Digital Salmon)
Project = Research grant (DigiSal, GenoSysFat)
Investigation = a particular biological process, phenomenon or thing
(typically corresponds to [plans for] one or more closely related papers)
Study = experiment whose design reflects a specific biological research question
Assay = standardized measurement or diagnostic experiment using a
...

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.

Initial configuration and parameters of the Bioleaching

This README file describes how the s-core / s-core+ analysis perl script is to be executed together with data files.

Metabolic networks with gene expression are researched under very different banners with different techniques. For example, there are the dynamic enzyme-cost Flux Balance Analysis (deFBA) [1], conditional Flux Balance Analysis [2], Metabolism and Expression models (ME models) [3], Resource Balance Analysis [4], etc. At their core, these methods can all understood as Resource Allocation Models (RAM) and while investigating their potential and their results, we encountered the problem of sharing
...

Method extraction of intracellular metabolites in Lactococcus lactis

Method extraction of intracellular metabolites in Lactococcus lactis