SOPs
What is a SOP?Filters
This file describes the naming system used to uniquely identify samples
Creator: Stephan Christel
Submitter: Stephan Christel
Sample preparation procedure for metabolic analysis on T. b. brucei 427 using LC/MS
Creator: Dong-Hyun Kim
Submitter: Dong-Hyun Kim
For the study of mRNA decay rates, transcription was inhibited with ActinomycinD, and RNA splicing with Sinefungin, at different time points, in the Matthews lab. rRNA depleted RNA was extracted from each of the samples in the Clayton lab, and sent for deep sequencing at the BioQuant facility in Heidelberg
Creator: Federico Rojas
Submitter: Federico Rojas
Sample preparation procedure for metabolic footprint analysis on T. b. brucei 427 using LC/MS
Creator: Dong-Hyun Kim
Submitter: Dong-Hyun Kim
Creators: Per Bruheim, Trond Ellingsen, Sunniva Hoel, Øyvind Jakobsen, Håvard Sletta, Alexander Wentzel, Anders Øverby, Strøm, A
Submitter: Jay Moore
Biomass sampling - SOP for sampling of biomass
Creator: Maksim Zakhartsev
Submitter: Maksim Zakhartsev
Winter conditions for 5 weeks (6th october – 10th November):
- Light on 12 hours per day
- Turn off water heating
- Feeding probably needs to be adjusted according to lower metabolism and feed intake in cold water
Spring condition (10th of November – 15th of December):
- Water heating on
- constant light (24hrs/day)
Vaccination (when and by whom?)
Transfer to sea-water (15th of December)
Last sampling for GenoSysFat in sea water (5th January – 25th of January).
Source: email with subject ...
Creators: Jon Olav Vik, Sandve Simen
Submitter: Jon Olav Vik
This is the Jupyter Notebook to allow editing and working with the code. It is a simple example of how a Selwyn test can look like if it is passed (1.) or failed (2.).
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
This is the pdf of the Jupyter Notebook to allow looking at the notebook without installing anything. It is a simple example of how a Selwyn test can look like if it is passed (1.) or failed (2.).
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
Creator: Michael Kohlstedt
Submitter: Michael Kohlstedt
This is a well-established, classical genetic method of constructing chromosomal monolysogenic fusions to a promoterless lacZ gene.
Creators: Alison Graham, Jeff Green, Robert Poole
Submitter: Alison Graham
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
Creators: Katrin Ripken, Sarah Kirstein
Submitter: Sarah Kirstein
Initial configuration and parameters of the Bioleaching
Creator: Stephan Christel
Submitter: Stephan Christel
Creators: Sarah Kirstein, Katrin Ripken
Submitter: Sarah Kirstein
Creators: Katrin Ripken, Esther Wenzel, Sarah Kirstein
Submitter: Sarah Kirstein
sampling procedure for mineral containing leaching experiments
Creator: Stephan Christel
Submitter: Stephan Christel
steps conducted to pellet cells for RNA and protein extraction
Creator: Stephan Christel
Submitter: Stephan Christel
Creator: Lars Wöhlbrand
Submitter: Lars Wöhlbrand
Creators: Daniel Wünsch, Patrick Becker
Submitter: Daniel Wünsch
Creator: Martijn Bekker
Submitter: The JERM Harvester
Method extraction of intracellular metabolites in Lactococcus lactis
Creator: Martijn Bekker
Submitter: The JERM Harvester
Creator: Martijn Bekker
Submitter: The JERM Harvester
Creator: Martijn Bekker
Submitter: The JERM Harvester
Creator: Martijn Bekker
Submitter: The JERM Harvester
Creator: Martijn Bekker
Submitter: The JERM Harvester
The reverse transcriptase synthesizes DNA, which complements the mRNA template (complementary DNA, cDNA). Cy3/Cy5-dCTP are incorporated into cDNA during Reverse transcription. The obtained Cy3/Cy5 cDNA are then competitively hybridised onto Agilent microarray slide and subsequently scanned.
Creator: Praveen kumar Sappa
Submitter: Praveen kumar Sappa
SOP for shake flask cultivation of B.Subtilis in Bacell-Sysmo
Creator: Praveen kumar Sappa
Submitter: Praveen kumar Sappa
SOP describing how to perform Dynamic Light Scattering (DLS) measurements with Gre2p in cuvettes using a Zetasizer Nano DLS reader.
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
SOP describing how to perform activity measurements (inital rates) with Gre2p in multiwell plates (96w) using an UV-Vis Plate reader (Synergy H1).
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
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
Standard Operating Procedure for human genomic DNA extraction ( copied from GEO DataSets GSM1375121)
Creators: Olga Krebs, Christiane Opitz
Submitter: Olga Krebs
SOP describing how to perform an ITC (recurrent) single injections experiment with a MicroCal PEAQ ITC by Malvern.
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
SOP describing how to perform an ITC binding experiment with a MicroCal PEAQ ITC by Malvern. Note: the DOIs from the Chemotion database for the synthesis of HK and NDK are missing in this version beacuse the DOIs do not exist yet (as of 27.04.21)
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
SOP describing how to perform an ITC multiple injections experiment with a MicroCal PEAQ ITC by Malvern.
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
SOP describing how to perform specific activity measurements with Gre2p in multiwell plates (96w) using an UV-Vis Plate reader (Synergy H1).
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
SOP describing the steps for use of the ITC device (MicroCal PEAQ ITC by Malvern).
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
General SOP for alpha-tubulin homology model building
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
SOP describing application of the Induced fit docking workflow to Trypanosoma and Leishmania alpha-tubulin receptors.
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Associated library SOP file with metadata template.
Creator: Rohola Hosseini
Submitter: Rohola Hosseini
Detailed description of the methods applied for metabolomic analyses of P. cordatum heat stress response
Creator: Carsten Reuse
Submitter: Carsten Reuse
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
General SOP for the webPIPSA workflow to study electrostatic potential differences of full alpha-tubulin homology models and various putative binding site regions
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Detailed description of the methods applied for proteomic analyses of P. cordatum heat stress response
Creator: Lars Wöhlbrand
Submitter: Lars Wöhlbrand
SOP for protein preparation steps performed for alpha-tubulin homology models (hydrogen addition, hydrogen bonding network optimization and energy minimization)
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
Creators: Katrin Ripken, Esther Wenzel, Sarah Kirstein
Submitter: Sarah Kirstein
SOP for bioleaching experiments carried out for microscopy analysis at UDE
Creators: Malte Herold, Soeren Bellenberg
Submitter: Malte Herold
Creator: Theresa Kouril
Submitter: Theresa Kouril
Creators: Katrin Ripken, Sarah Kirstein
Submitter: Sarah Kirstein
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
Creators: Sarah Kirstein, Katrin Ripken, Esther Wenzel
Submitter: Sarah Kirstein
Creator: Theresa Kouril
Submitter: Theresa Kouril
Extraction procedure and lipid analysis.
Creators: Zdenka Bartosova, Jon Olav Vik, Per Bruheim, Thomas Harvey
Submitter: Zdenka Bartosova
Creator: Theresa Kouril
Submitter: Theresa Kouril
Creator: Theresa Kouril
Submitter: Theresa Kouril
ClosTron mutants should always be subjected to Southern blot analysis to ensure that only one intron insertion has occurred.
Creators: Ying Zhang, Nigel Minton
Submitter: Ying Zhang
Creators: Trond Ellingsen, Øyvind Jakobsen, Per Bruheim, Håvard Sletta, Anders Øverby, Sven Even Borgos, Sunniva Hoel, Alexander Wentzel
Submitter: Jay Moore
Standard Operating Procedure (SOP) for integration of MESI-STRAT sequence data stored in MESI-SEEK into ENA
Creator: Olga Krebs
Submitter: Olga Krebs
Creators: Holger Janssen, Tomas Fiedler
Submitter: Holger Janssen
SOPs related with medium composition, fermentation and stocking of S. solfataricus.
Creator: Pawel Sierocinski
Submitter: Pawel Sierocinski
Standard procedure regarding intracellular metabolome analysis using GC-MS.
Creator: Pawel Sierocinski
Submitter: Pawel Sierocinski
Protocol for RNA isolation, cDNA synthesis and labeling and hybridization and cleanup of Sulfolobus solfataricus microarray
Creator: Pawel Sierocinski
Submitter: Pawel Sierocinski
Standard operating procedures regarding iTraq based proteomics.
Creator: Pawel Sierocinski
Submitter: Pawel Sierocinski
Creators: Theresa Kouril, Andreas Albersmeier, CeBiTech, University Bielefeld, Germany; Jörn Kalinowski, CeBiTech, University Bielefeld;
Submitter: Theresa Kouril
Creator: Theresa Kouril
Submitter: Theresa Kouril
Protein extraction, iTRAQ labeling, peptides separation, mass spectrometry and data analysis
Creators: Theresa Kouril, Phil Wright, Trong Khoa Pham
Submitter: Theresa Kouril
This SOP describes the SUMO procedure for determining B-galactosidase activities.
Creator: Matthew Rolfe
Submitter: Matthew Rolfe
This document describes the chemostat conditions to run comparable experiments in different bioreactors in different labs.
Creator: Sonja Steinsiek
Submitter: Sonja Steinsiek
This file describes how to isolate mRNA from E. coli using the kit from Epicentre, for gene expression analysis via RT-PCR
Creator: Sonja Steinsiek
Submitter: Sonja Steinsiek
This SOP describes the preparation of E. coli RNA
Creator: Matthew Rolfe
Submitter: Matthew Rolfe
This protocol describes the transcriptional profiling of E. coli cultures using microarrays. The protocol utilises RNA isolated as described in another SOP (SUMO RNA isolation from E. coli) and with hybridisation to Ocimum Ocichip E. coli K-12 microarrays.
Creator: Matthew Rolfe
Submitter: Matthew Rolfe