SOPs
steps conducted to pellet cells for RNA and protein extraction
Creator: Stephan Christel
Submitter: Stephan Christel
This file describes the naming system used to uniquely identify samples
Creator: Stephan Christel
Submitter: Stephan Christel
SOP for extracting DNA, RNA and Proteins from the mineral pellet of a bioleaching culture using hot acidic phenol. Current draft.
Creators: Malte Herold, Mario Vera, Soeren Bellenberg
Submitter: Malte Herold
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
sampling procedure for mineral containing leaching experiments
Creator: Stephan Christel
Submitter: Stephan Christel
This file contains the detailed experimental protocol to isolate nuclei from murine hearts.
Creators: Markus Wolfien, Anne-Marie Galow
Submitter: Markus Wolfien
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.
Creator: Markus Wolfien
Submitter: Markus Wolfien
Master Bash script to launch Molecular Dynamics when running the Simulation part of Simulation Foundry. Make sure you followed "Preparations" instructions! Read the Manual!
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
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
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 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.
Creator: Vânia Pobre
Submitter: Vânia Pobre
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
Creators: Niels Zondervan, Luis Serrano, Maria Lluch, Eva Yus
Submitter: Niels Zondervan
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
Creator: Niels Zondervan
Submitter: Niels Zondervan
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 ...
Creators: Jon Olav Vik, Natalie Stanford
Submitter: Jon Olav Vik
Describes the cultivation-, washing- and electroporation-steps required in order to transform bacterial cells with DNA.
Creator: Maximilian Bahls
Submitter: Maximilian Bahls
Describes the steps required in order to run an error-prone PCR (epPCR) for the creation of DNA libraries of a given template gene.
Creator: Maximilian Bahls
Submitter: Maximilian Bahls
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.
Creators: Linde Kampers, Fons Stams
Submitter: Linde Kampers
Standard Operating Procedure for human genomic DNA extraction ( copied from GEO DataSets GSM1375121)
Creators: Olga Krebs, Christiane Opitz
Submitter: Olga Krebs
Initial configuration and parameters of the Bioleaching
Creator: Stephan Christel
Submitter: Stephan Christel
This README file describes how the s-core / s-core+ analysis perl script is to be executed together with data files.
Creators: Eivind Almaas, Marius Eidsaa
Submitter: Eivind Almaas
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 ...
Creators: Henning Lindhorst, Alexandra-M. Reimers
Submitter: Henning Lindhorst
Method extraction of intracellular metabolites in Lactococcus lactis
Creator: Martijn Bekker
Submitter: The JERM Harvester
Method extraction of intracellular metabolites in Lactococcus lactis
Creator: Martijn Bekker
Submitter: The JERM Harvester
Method for transformation of plasmids into Lactococcus lactis
Creator: Martijn Bekker
Submitter: The JERM Harvester
Method for synthesis of LAB-medium sued for the SYSMO-LAB project
Creator: Martijn Bekker
Submitter: The JERM Harvester
Method for analysis of various organic acids in the medium
Creator: Martijn Bekker
Submitter: The JERM Harvester
Creators: Theresa Kouril, Andreas Albersmeier, CeBiTech, University Bielefeld, Germany; Jörn Kalinowski, CeBiTech, University Bielefeld;
Submitter: Theresa Kouril