SOPs
What is a SOP?Filters
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.
Creator: Malte Herold
Submitter: Malte Herold
Describes the workflow used for preparation of a 16S rRNA gene amplicon (V3-V4 region) Library for sequencing on a MiSeq platform (Illumina) using V3 sequencing chemistry with 300 base pairs paired-end reads.
Creators: Inga Leena Angell, Jon Olav Vik, Graceline Tina Kirubakaran, Sahar Hassani
Submitter: Inga Leena Angell
A kinetic model that describess the activation of a dimeric efflux system that could bind either GSH or SLG
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
This SOP describes the in silico ADME-Tox property prediction with QikProp for prepared pteridine ligands.
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
A model to describe aggregation of homomeric protein complexes in mechanosensitive channels in E.coli.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
SOP for measurement of ALD activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
SOP for growing yeast in anaerobic conditions
Creator: Maksim Zakhartsev
Submitter: Maksim Zakhartsev
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).
Creator: Maximilian Bahls
Submitter: Maximilian Bahls
This HPLC method uses a isocratic method and a RI detector to identify and quantify almost all excreted catabolic metabolites.
Creator: Martijn Bekker
Submitter: Martijn Bekker
Method for analysis of various organic acids in the medium
Creator: Martijn Bekker
Submitter: The JERM Harvester
Measurements of K+ retained in the cytoplasm using flame photometry.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
A procedure to analyse the genomic interaction of E.coli RNA polymerase (RNAP) upon methylglyoxal (MG) stress, a toxic keto-aldehyde by-product of metabolism.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
Master Bash script to launch Molecular Dynamics when running the Analysis part of Simulation Foundry. Make sure you followed "Preparations" instructions! Read the Manual!
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
Assay methodologies for individual glycolytic isoenzymes from the Mendes Group, University of Manchester, UK
Creator: Hanan Messiha
Submitter: Walter Glaser
The kit is used for the quantitative detection of ATP in yeast cells by luciferase driven bioluminescence. ATP extraction is done by boiling cells in TE buffer.
Creators: Martin Valachovic, Cornelia Klein
Submitter: Walter Glaser
Protocol for transfer of plasmids into Clostridium acetobutylicum ATCC 824 by electroporation
Creators: None
Submitter: Ying Zhang
Purpose: Cation content analysis - protocol
Creator: Clara Navarrete
Submitter: The JERM Harvester
The reverse transcriptase synthesizes DNA, which complements the mRNA template.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
Creators: Per Bruheim, Trond Ellingsen, Sunniva Hoel, Øyvind Jakobsen, Håvard Sletta, Alexander Wentzel, Anders Øverby, Strøm, A
Submitter: Jay Moore
Cloning and heterologous expression of gluconeogenic enzymes from S. solfataricus in E. coli
Creators: Jacky Snoep, Theresa Kouril
Submitter: Jacky Snoep
A refined and streamlined procedure to generate mutant in a wide range of different clostridial species, using group II intron retargeting methodologies.
Creators: Ying Zhang, Nigel Minton
Submitter: Ying Zhang
Creators: Per Bruheim, Trond Ellingsen, Sunniva Hoel, Øyvind Jakobsen, Håvard Sletta, Alexander Wentzel, Anders Øverby, Strøm, A
Submitter: Jay Moore
To induce kdpFABC expression, cells are cultivated in K10 minimal medium (10mM K+) were shifted into K+ limiting growth medium (K0), containing 20 μM K+ by filtration.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
SOP for the cultivation conditions of Plasmodium falciparum, including the protocol for synchronisation.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Creator: Martijn Bekker
Submitter: The JERM Harvester
This method describes how to derivatize the N-glutathionylspermidine and trypanothione produced by T. brucei trypanothione synthetase under in vivo-like conditions
Creator: Alejandro Leroux
Submitter: Alejandro Leroux
This is the Jupyter Notebook to allow editing and working with the code.
Design an initial rate experiment in four steps
This script aims to help you design high-quality initial rate experiments. It uses the Michaelis-Menten equation to simulate data for an enzyme with unknown enzyme reaction parameters. Four steps are needed:
- Estimate the enzyme reaction parameters
Input: estimates of Km and vmax
and indicate the enzyme concentration concentration you are planning to use. If you have no ...
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
This is the pdf of the Jupyter Notebook to allow looking at the notebook without installing anything.
Design an initial rate experiment in four steps
This script aims to help you design high-quality initial rate experiments. It uses the Michaelis-Menten equation to simulate data for an enzyme with unknown enzyme reaction parameters. Four steps are needed: 1. Estimate the enzyme reaction parameters
Input: estimates of Km and vmax
and indicate the enzyme concentration concentration you are planning ...
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
Sample preparation - SOP for sampling, preparation of cell-free extracts, and determination of total extracted protein
Creator: Femke Mensonides
Submitter: Maksim Zakhartsev
Sample preparation - SOP for sampling, preparation of cell extracts, and general assay set-up
Creator: Femke Mensonides
Submitter: Maksim Zakhartsev