SOPs
What is a SOP?Filters
Creator: Charles Demurjian
Submitter: Charles Demurjian
DownloadCreator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creators: None
Submitter: Charles Demurjian
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Submitter: Charles Demurjian
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Submitter: Charles Demurjian
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Submitter: Charles Demurjian
Creators: None
Submitter: Charles Demurjian
Creators: None
Submitter: Charles Demurjian
Creators: None
Submitter: Charles Demurjian
Creators: None
Submitter: Charles Demurjian
Creators: None
Submitter: Charles Demurjian
Creators: None
Submitter: Charles Demurjian
Creators: None
Submitter: Charles Demurjian
Creators: None
Submitter: Charles Demurjian
Creators: None
Submitter: Charles Demurjian
Creators: None
Submitter: Charles Demurjian
Creators: None
Submitter: Charles Demurjian
Creators: None
Submitter: Charles Demurjian
Creators: None
Submitter: Charles Demurjian
Creators: None
Submitter: Charles Demurjian
Creators: None
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Lars Wöhlbrand
Submitter: Lars Wöhlbrand
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Diletta Arceri
Submitter: Diletta Arceri
Creator: Andrea Rizzo
Submitter: Andrea Rizzo
Creator: Andrea Rizzo
Submitter: Andrea Rizzo
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
General SOP of the overall study - contains info from both the manuscript and supplementary information packet.
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Detailed description of the methods applied for proteomic analyses of P. cordatum heat stress response
Creator: Lars Wöhlbrand
Submitter: Lars Wöhlbrand
Detailed description of the methods applied for metabolomic analyses of P. cordatum heat stress response
Creator: Carsten Reuse
Submitter: Carsten Reuse
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Standard Operating Procedure (SOP) for integration of MESI-STRAT sequence data stored in MESI-SEEK into ENA
Creator: Olga Krebs
Submitter: Olga Krebs
A Standard Operating Procedure (SOP) is a document consisting of step-by-step information on how to execute a task. An existing SOP may need to just be modified and updated.
Creator: Olga Krebs
Submitter: Deleted submitter
Creator: Theresa Kouril
Submitter: Theresa Kouril
Creator: Theresa Kouril
Submitter: Theresa Kouril
Creator: Theresa Kouril
Submitter: Theresa Kouril
Creator: Theresa Kouril
Submitter: Theresa Kouril
Creators: Christoff Odendaal, Barbara Bakker
Submitter: Christoff Odendaal
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Standard Operating Procedure for human genomic DNA extraction ( copied from GEO DataSets GSM1375121)
Creators: Olga Krebs, Christiane Opitz
Submitter: Olga Krebs
SOP describing application of the Induced fit docking workflow to Trypanosoma and Leishmania alpha-tubulin receptors.
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
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
General SOP for alpha-tubulin homology model building
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
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
An overview of MIHCSME template components.
Creator: Rohola Hosseini
Submitter: Rohola Hosseini
There are three files:
- executable.py
- functions.py
- plots.py
The first file leads you through my data creation and processing step by step. You can choose how many of my data you want to use or reproduce by yourself.
The executable-file needs the functions from "functions" and "plots" in order to run correctly.
Creator: Aaron Laier
Submitter: Aaron Laier
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
This file is associated with performed study and describes protocols used.
Creator: Rohola Hosseini
Submitter: Rohola Hosseini
Associated library SOP file with metadata template.
Creator: Rohola Hosseini
Submitter: Rohola Hosseini
Creator: Flora D'Anna
Submitter: Flora D'Anna
Creator: Jake Schissel
Submitter: Jake Schissel
Creator: Jake Schissel
Submitter: Jake Schissel
Creator: Jake Schissel
Submitter: Jake Schissel
Creator: Jake Schissel
Submitter: Jake Schissel
Creator: Jake Schissel
Submitter: Jake Schissel
Creator: Jake Schissel
Submitter: Jake Schissel
Creator: Jake Schissel
Submitter: Jake Schissel
Creator: Jake Schissel
Submitter: Jake Schissel
Creators: Sarah Kirstein, Katrin Ripken
Submitter: Sarah Kirstein
Creator: Lars Wöhlbrand
Submitter: Lars Wöhlbrand
Creators: Sarah Kirstein, Katrin Ripken, Esther Wenzel
Submitter: Sarah Kirstein
Creators: Katrin Ripken, Esther Wenzel, Sarah Kirstein
Submitter: Sarah Kirstein
Creators: Katrin Ripken, Sarah Kirstein
Submitter: Sarah Kirstein
Creators: Katrin Ripken, Esther Wenzel, Sarah Kirstein
Submitter: Sarah Kirstein
Creators: Katrin Ripken, Sarah Kirstein
Submitter: Sarah Kirstein
Creator: Jake Schissel
Submitter: Jake Schissel
Creator: Jake Schissel
Submitter: Jake Schissel
Creator: Jake Schissel
Submitter: Jake Schissel
Creator: Jake Schissel
Submitter: Jake Schissel
Creator: Jake Schissel
Submitter: Jake Schissel
Creator: Jake Schissel
Submitter: Jake Schissel
Standard Operating Procedure describes the labeling of eukaryotic RNA with aminoallyl labeled nucleotides via first strand cDNA synthesis followed by a coupling of the aminoallyl groups to either Cyanine 3 or 5 (Cy 3/Cy5) fluorescent molecules (published by The Institute For Genomic Research
Creators: Olga Krebs, Jeremy Hasseman , Emily Chen, Ivana Yang
Submitter: Olga Krebs
Creators: Daniel Wünsch, Patrick Becker
Submitter: Daniel Wünsch
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
This is the Jupyter Notebook to allow editing and working with the code. It is a simple example of how a progress curve experiment can look like.
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 progress curve experiment can look like.
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
This is the pdf of the Jupyter Notebook to allow looking at the notebook without installing anything.
NOTE THAT this pdf may be mangled when viewed on FAIRDOMHub, but should look fine when downloaded.
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
This is a zip file containing all the files and folders needed to analyse raw data, fit initial rates and create a "Michaelis-Menten plot". Instructions on usage are added in the notebook.
Creator: Gudrun Gygli
Submitter: Gudrun Gygli
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
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
Next-Gen GPT Assay Protocol
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Collection of Tissues at Necropsy of Short-Term Animals
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Medium-Term Tissue Collection at Necropsy
Creator: Dikshant Pradhan
Submitter: Dikshant Pradhan
Extraction procedure and lipid analysis.
Creators: Zdenka Bartosova, Jon Olav Vik, Per Bruheim, Thomas Harvey
Submitter: Zdenka Bartosova
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
Source: Tom Harvey [E- mail from Jon Olav 19 May 2016]
Creators: Graceline Tina Kirubakaran, Thomas Harvey, Jacob Seilø Torgersen
Submitter: Graceline Tina Kirubakaran
Use this template when you upload RNA sequencing data. Email : 31 May 2016 More columns need to be added PE/SE etc?
Creators: Graceline Tina Kirubakaran, Jon Olav Vik, Thomas Harvey, Sandve Simen, Hanne Hellerud Hansen
Submitter: Graceline Tina Kirubakaran
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
Describes how the DNA was isolated from salmon intestinal samples before preparations of 16S rRNA gene amplicons for the Illumina MiSeq system.
Creators: Stuart Owen, Sahar Hassani, RAGNHILD ÅNESTAD, Jesse van Dam, Dagmar Waltemath, Kristina Vagonyte-Hallan, Kristil Sundsaasen, Natalie Stanford, Lars Snipen, Sandve Simen, Jacob Seilø Torgersen, Inga Leena Angell, Dominic Nanton, Vitor Martins dos Santos, Torgeir R. Hvidsten, Thomas Harvey, Hanne Hellerud Hansen, Fabian Grammes, Arne Gjuvsland, Gareth Gillard, Graceline Tina Kirubakaran, Jon Olav Vik
Submitter: Inga Leena Angell
Gre2p activity monitored by NADPH absorbance using different enzyme concentrations. Activity is measured after different storage conditions (treatments) and in presence of different amounts of tween.
A python workflow is used to analyse the data and create a plot where the outcomes of the Selwyn test are plotted. It requires the following directory structure:
./Sewlyn_test_forS19.py ./tween/M1.csv ./tween/M2.csv ./tween/M3.csv ./tween/M4.csv ./treatments/M1.csv ./treatments/M2.csv ./treatments/M3.csv ...
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
Gre2p activity monitored by NADPH absorbance using different enzyme concentrations. Activity is measured after different storage conditions (treatments) and in presence of different amounts of tween. Also analysis of DLS data of homogeneity of Gre2p samples measured before and after these treatments.
A python workflow is used to analyse the data and create a plot of the data. It requires the following directory structure:
./Script_for_S13andS18.py ./Script_for_S22.py ./Script_for_S15.py
and as ...
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
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
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.
Creator: Anne-Marie Galow
Submitter: Anne-Marie Galow
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 an ITC (recurrent) single injections experiment with a MicroCal PEAQ ITC by Malvern.
Creators: Gudrun Gygli, Felix Ott
Submitter: Gudrun Gygli
Python workflow for the analysis of ITC-BIND, ITC-MIM and ITC-(r)SIM experiments. Organized in a *.zip folder. Requires the following directory structure:
./ITC_analysis.py ./input/BINDING/.apj ./input/BINDING/.csv ./input/KINETICS/.apj ./input/KINETICS/.csv ./scripts/binding_neu.py ./scripts/kinetics_neu.py
And can be executed by running python ITC_analysis.py in the directory. Filenames for the input *.apj and *.csv files are defined in ITC_analysis.py. The output directory is written by ...
Creator: Gudrun Gygli
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 the steps for use of the ITC device (MicroCal PEAQ ITC by Malvern).
Creator: Gudrun Gygli
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 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
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.
Creators: Anne-Marie Galow, Sophie Kussauer, Markus Wolfien
Submitter: Anne-Marie Galow
This SOP describes the preparation of pteridine ligand 3D structures from SMILES or other input formats with the LigPrep routine as embedded in Schrödinger Maestro for usage in docking runs and in silico ADME-Tox property prediction.
Creators: Ina Poehner, Rebecca Wade, Joanna Panecka-Hofman
Submitter: Ina Poehner
This SOP describes the docking receptor preparation of PTR1 and DHFR receptor PDB files, performed with the Maestro Protein PrepWizard and the Glide grid generation routine. The optional identification and integration of conserved structural water molecules with the WatCH tool is also covered.
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
This SOP describes the in silico ADME-Tox property prediction with QikProp for prepared pteridine ligands.
Creators: Ina Poehner, Rebecca Wade
Submitter: Ina Poehner
This SOP describes the docking of pteridine libraries into PTR1 or DHFR target receptors, using Glide in Schrödinger Maestro with the XP (eXtra Precision) protocol.
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
This SOP describes the docking of pteridine libraries into PTR1 or DHFR target receptors, using Glide and Prime in Schrödinger Maestro as part of the Induced Fit workflow to allow for receptor side chain reorganization upon ligand binding.
Creators: Ina Poehner, Joanna Panecka-Hofman, Rebecca Wade
Submitter: Ina Poehner
Instructions and details on the data analysis workflow.
Creators: Gudrun Gygli, Juergen Pleiss, Xinmeng Xu
Submitter: Gudrun Gygli
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.
Creator: Anne-Marie Galow
Submitter: Anne-Marie Galow
Creator: Markus Wolfien
Submitter: Markus Wolfien
This guidlines has been developed by Rita Volkers from Wageningen University for IBISBA project, as example to use
Creators: Olga Krebs, Rita Volkers
Submitter: Olga Krebs
Aceton precipitation and protein digestion for proteomic workflow
Creators: Malte Herold, Mohamed El Hajjami
Submitter: Malte Herold
SOP for bioleaching experiments carried out for microscopy analysis at UDE
Creators: Malte Herold, Soeren Bellenberg
Submitter: Malte Herold
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
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
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
Detection of small RNAs by blot hybridization.
Creator: Vânia Pobre
Submitter: Vânia Pobre
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
Creator: Susana Domingues
Submitter: Susana Domingues
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
External LinkDescribes 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
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
Protein extraction, iTRAQ labeling, peptides separation, mass spectrometry and data analysis
Creators: Theresa Kouril, Phil Wright, Trong Khoa Pham
Submitter: Theresa Kouril
Creator: Tomas Fiedler
Submitter: Tomas Fiedler
Creator: Tomas Fiedler
Submitter: Tomas Fiedler
Protocol for applying a glucose perturbation in Streptococcus pyogenes.
Creator: Martijn Bekker
Submitter: Martijn Bekker
Perturbation of starved cells with glucose. Concentrations of intra- and extracellular metabolites are followed in time.
Creator: Martijn Bekker
Submitter: Martijn Bekker
Creator: Martijn Bekker
Submitter: The JERM Harvester
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
A protocol for acidic quenching of lactic acid bacteria used for analyses of intracellular metabolites.
Creator: Martijn Bekker
Submitter: Martijn Bekker
This protocol for applying glucose perturbations works for Lactococcus lactis and Enterococcus faecalis
Creator: Martijn Bekker
Submitter: Martijn Bekker
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
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).
Creator: Natalie Stanford
Submitter: Natalie Stanford
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.
Creator: Natalie Stanford
Submitter: Natalie Stanford
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.
Creator: Natalie Stanford
Submitter: Natalie Stanford
SOP for the determination of external metabolites (Glc, Pyr, Gly, Lac) in intact trophozoite incubations, and for the determination of intracellular metabolite concentrations.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
SOP for the cultivation conditions of Plasmodium falciparum, including the protocol for synchronisation.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
SOP for measurement of G3PDH activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
SOP for measurement of ALD activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
SOP for measurement of glucose transport activity in intact trophozoites.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
SOP for measurement of GAPDH activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
SOP for measurement of ENO activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
SOP for measurement of HK activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
SOP for measurement of PFK activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
SOP for measurement of LDH activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
SOP for measurement of PGK activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
SOP for measurement of PK activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
SOP for measurement of PGM activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
SOP for measurement of PGI activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
SOP for measurement of PGM activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
SOP for measurement of TPI activity in extracts.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
SOP for the isolation of intact Plasmodium falciparum trophozoites from infected red blood cells and the preparation of a cell free extract that can be used for kinetic analyses.
Creators: Dawie van Niekerk, Jacky Snoep
Submitter: Dawie van Niekerk
Creator: Theresa Kouril
Submitter: Theresa Kouril
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
Isolation of total RNA from Bacillus Subtilis using phenol-chloroform extraction method by maintaining cryogenec conditions initailly to prevent RNA degradation. Quality of the obtained RNA is then tested with Agilent Bioanalyser before proceeding for gene expression analysis.
Creator: Praveen kumar Sappa
Submitter: Praveen kumar Sappa
An overview of creating MAGE-TAB compliant spreadsheets for transcriptomics data in SysMO SEEK
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
The procedure describes the preparation of fluorescent DNA probes from human mRNA or total RNA.
Creator: Olga Krebs
Submitter: Olga Krebs
This is a protocol for determining the activity of the T. brucei Trypanothione synthetase under in vivo-like conditions.
Creators: Alejandro Leroux, Luise Krauth-Siegel
Submitter: Alejandro Leroux
This method describes the preparation of the in vivo-like buffer for the measurement of bloodstream T. brucei recombinant enzymes under pseudo-physiological conditions.
Creators: Alejandro Leroux, Luise Krauth-Siegel
Submitter: Alejandro Leroux
Preparation of cell free extracts of the recombinant E. coli strains expressing the gluconeogenic S. solfataricus enzymes.
Creators: Jacky Snoep, Theresa Kouril
Submitter: Jacky Snoep
Cloning and heterologous expression of gluconeogenic enzymes from S. solfataricus in E. coli
Creators: Jacky Snoep, Theresa Kouril
Submitter: Jacky Snoep
Purification of gluconeogenic enzymes from S. solfataricus in recombinant E.coli extracts
Creators: Jacky Snoep, Theresa Kouril
Submitter: Jacky Snoep
This assay uses a dual-wavelength spectrophotometer to quantify cytochromes present in the E. coli respiratory chain.
Creators: Alison Graham, Robert Poole, Jeff Green
Submitter: Alison Graham
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
The phosphorylation level of a particular protein can be determined using a procedure based upon western immunoblotting, with Phos-tag™ reagent present in the SDS-PAGE gel. The Phos-tag™ reagent, supplied in the form of Phos-tag™ acrylamide (Wako Pure Chemical Industries, AAL-107), causes proteins to be resolved both on the basis of size and phosphorylation state. This means that phosphorylated and de-phosphorylated forms of the same protein can be distinguished.
Creator: Matthew Rolfe
Submitter: Matthew Rolfe
The Gene-doctoring method of lambda-red deletion (Lee et al., 2009) was modified slightly to create chromosomal mutations of fnr.
Creator: Matthew Rolfe
Submitter: Matthew Rolfe
This method describes how one can quench metabolism of Escherichia coli and extract metabolites from many kinds of metabolite classes like: nucleotides, sugar-phosphates, organic acids ....
Creator: Stefan Stagge
Submitter: Stefan Stagge
Sample preparation procedure for metabolic analysis on T. b. brucei 427 using LC/MS
Creator: Dong-Hyun Kim
Submitter: Dong-Hyun Kim
Labelling and extraction procedure for uniformly 13C-labelled E. coli (MG1655) for absolute quantification using isotope dilution technique by LC-MS
Creator: Dong-Hyun Kim
Submitter: Dong-Hyun Kim
Sample preparation procedure for metabolic footprint analysis on T. b. brucei 427 using LC/MS
Creator: Dong-Hyun Kim
Submitter: Dong-Hyun Kim
Creator: Federico Rojas
Submitter: Federico Rojas
Assay methodologies for individual glycolytic isoenzymes from the Mendes Group, University of Manchester, UK
Creator: Hanan Messiha
Submitter: Walter Glaser
This is the general protocol for the glycolytic enzyme measurements. Detailed Information for each Enzyme can be found in the SOP: Assays for measuring the activities of the individual glycolytic isoenzymes of Saccharomyces cerevisiae
Creator: Hanan Messiha
Submitter: Walter Glaser
Creator: John Raedts
Submitter: John Raedts
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
Protocol for transfer of plasmids into Clostridium acetobutylicum ATCC 824 by electroporation
Creators: None
Submitter: Ying Zhang
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
A protocol to improve conventional, recombination-based gene knock-out methodologies thtough the provision of negative selection markers, pyrE or codA.
Creators: Ying Zhang, Nigel Minton
Submitter: Ying Zhang
Protocol for transfer of plasmids into Clostridium spp. by conjugation
Creators: Ying Zhang, Nigel Minton
Submitter: Ying Zhang
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
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
This SOP describes the preparation of E. coli RNA
Creator: Matthew Rolfe
Submitter: Matthew Rolfe
Creator: Michael Kohlstedt
Submitter: Michael Kohlstedt
SOP for growing yeast in anaerobic conditions
Creator: Maksim Zakhartsev
Submitter: Maksim Zakhartsev
Biomass sampling - SOP for sampling of biomass
Creator: Maksim Zakhartsev
Submitter: Maksim Zakhartsev
Metabolic perturbations - SOP for metabolic perturbations (i.e. glucose pulse)
Creator: Maksim Zakhartsev
Submitter: Maksim Zakhartsev
Yeast strains used in the project
Creator: Maksim Zakhartsev
Submitter: Maksim Zakhartsev
General protocol for measuring the kinetic parameters of the purified glycolytic enzymes from Saccharomyces cerevisiae - SOP for measuring the kinetic parameters of the purified glycolytic isoenzymes
Creator: Hanan Messiha
Submitter: Maksim Zakhartsev
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
We routinely select specific RNAi gene targets (400–600 bp) and primers using the RNAit software http://trypanofan.path.cam.ac.uk/software/RNAit.html. A single pair of PCR primers are designed that incorporate four selected restriction sites (not present in the RNAi target fragment) such that a single PCR product can be differentially digested and sequentially cloned. For example, using MCS1/2, the following primers could be used to clone antisense followed by sense fragments: Primer 1, XbaI–BamHI-5′ ...
Creator: Federico Rojas
Submitter: Federico Rojas
SOP for extracellular metabolite measurment
Creator: Hanna Meyer
Submitter: Hanna Meyer
Written Standard Operating Procedures provide workers with the operational information necessary to perform a job properly and ensure consistency in the operations. Standard Operating Procedures provide a historical record of steps in the how, why and when and serve as a training tool for teaching users.
Creator: Olga Krebs
Submitter: Olga Krebs
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
Creator: Lina Patricia Barreto Parra
Submitter: Lina Patricia Barreto Parra
Creator: Holger Janssen
Submitter: The JERM Harvester
Creators: Holger Janssen, Tomas Fiedler
Submitter: Holger Janssen
Creators: Trond Ellingsen, Øyvind Jakobsen, Per Bruheim, Håvard Sletta, Anders Øverby, Sven Even Borgos, Sunniva Hoel, Alexander Wentzel
Submitter: Jay Moore
Creators: Trond Ellingsen, Øyvind Jakobsen, Per Bruheim, Håvard Sletta, Anders Øverby, Sven Even Borgos, Sunniva Hoel, Alexander Wentzel
Submitter: Jay Moore
Creators: Trond Ellingsen, Øyvind Jakobsen, Per Bruheim, Håvard Sletta, Anders Øverby, Sven Even Borgos, Sunniva Hoel, Alexander Wentzel
Submitter: Jay Moore
Creators: Louise Thomas, Maggie Smith
Submitter: Jay Moore
Creators: Louise Thomas, Maggie Smith
Submitter: Jay Moore
Creators: Louise Thomas, Maggie Smith
Submitter: Jay Moore
Creators: Louise Thomas, Maggie Smith
Submitter: Jay Moore
Creators: Louise Thomas, Maggie Smith
Submitter: Jay Moore
Creators: Per Bruheim, Trond Ellingsen, Sunniva Hoel, Øyvind Jakobsen, Håvard Sletta, Alexander Wentzel, Anders Øverby, Strøm, A
Submitter: Jay Moore
Creators: Per Bruheim, Trond Ellingsen, Sunniva Hoel, Øyvind Jakobsen, Håvard Sletta, Alexander Wentzel, Anders Øverby, Strøm, A
Submitter: Jay Moore
Creators: Per Bruheim, Trond Ellingsen, Sunniva Hoel, Øyvind Jakobsen, Håvard Sletta, Alexander Wentzel, Anders Øverby, Strøm, A
Submitter: Jay Moore
Creators: Per Bruheim, Trond Ellingsen, Sunniva Hoel, Øyvind Jakobsen, Håvard Sletta, Alexander Wentzel, Anders Øverby, Strøm, A
Submitter: Jay Moore
Creators: Per Bruheim, Trond Ellingsen, Sunniva Hoel, Øyvind Jakobsen, Håvard Sletta, Alexander Wentzel, Anders Øverby, Strøm, A
Submitter: Jay Moore
Creators: Per Bruheim, Trond Ellingsen, Sunniva Hoel, Øyvind Jakobsen, Håvard Sletta, Alexander Wentzel, Anders Øverby, Strøm, A
Submitter: Jay Moore
Creators: Per Bruheim, Trond Ellingsen, Sunniva Hoel, Øyvind Jakobsen, Håvard Sletta, Alexander Wentzel, Anders Øverby, Strøm, A
Submitter: Jay Moore
This protocol is designed to prepare sufficient amounts of high-quality total RNA from the yeast saccharomyces cerevisiae grown in liquid culture for analysis on microarrays.
Creators: Walter Glaser, Christa Gregori
Submitter: Walter Glaser
Creator: Martijn Bekker
Submitter: The JERM Harvester
Creator: Sonja Steinsiek
Submitter: The JERM Harvester
Creator: Katja Bettenbrock
Submitter: The JERM Harvester
Creator: Martijn Bekker
Submitter: The JERM Harvester
Purpose: PROTEIN EXTRACTION FOR 2-DE BASED PROTEOMIC EXPERIMENTS. 2. Membrane proteins
Creator: Miguel Curto Rubio
Submitter: The JERM Harvester
Purpose: PROTEIN EXTRACTION FOR 2-DE BASED PROTEOMIC EXPERIMENTS. 1. Citosoluble proteins
Creator: Miguel Curto Rubio
Submitter: The JERM Harvester
Purpose: Cation content analysis - protocol
Creator: Clara Navarrete
Submitter: The JERM Harvester
Purpose:
Creator: Jose Ramos
Submitter: The JERM Harvester
SOP for ß-Galactosidase assay.
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
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 document describes the chemostat conditions to run comparable experiments in different bioreactors in different labs.
Creator: Sonja Steinsiek
Submitter: Sonja Steinsiek
SOPs related with medium composition, fermentation and stocking of S. solfataricus.
Creator: Pawel Sierocinski
Submitter: Pawel Sierocinski
MIAPE (Minimum Information About a Proteomics Experiment) is the recommended format for proteomics data in SysMO-SEEK. The document attached provides more information and links to tools and resources.
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
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
A model to describe the effect of K+ uptake by KdpFABC on the two-component system KdpD/KdpE, which enables the identification of control principles of the Kdp system
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
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
Cells were harvested from culture keeping the cells cold to quench the physiological condition of RNA and the cells were mechanically disrupted. RNA was isolated from the cells by conventional acid-phenol method and the quality was checked by Agilent bioanalyser.
Creator: Praveen kumar Sappa
Submitter: Praveen kumar Sappa
This SOP describes the SUMO procedure for determining B-galactosidase activities.
Creator: Matthew Rolfe
Submitter: Matthew Rolfe
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 defines the format of SOPs used in the SUMO consortium.
Creator: Michael Ederer
Submitter: Michael Ederer
A model for translation elongation, which allows the prediction of how different conditions and parameters affect the rate and throughput of translation.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
A model to describe aggregation of homomeric protein complexes in mechanosensitive channels in E.coli.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
Measurement of the transmembrane pH gradient and thus pHi, when the external pH is known.
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
SOP used for detecting non influential parameters and interactions in non linear dynamical models. These parameters can be estabilished which allows the prioritization of parameters that can be subsequently estimated using robust global optimizations methods.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
The model describes the series of chemical reactions in MG detoxification pathway, allowing one to predict the flux of all compounds produced during detoxification.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
Mathematical model of pH buffering, which allows the prediction of how the buffering capacity depends on the cytoplasm's composition, for any number of buffers.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
Method of how to perform the purification of glyoxalase II as well as kinetics assays.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
A method of how to measure methylglyoxal present in the growth medium.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
Measurements of K+ retained in the cytoplasm using flame photometry.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
The fluorescent DNA-binding dye used in qRT-PCR binds to all kinds of double stranded DNA. To prevent false-positive results, the RNA is treated with DNase to remove remaining DNA.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
Quantitative real-time PRC is used to compare kdpFABC expression between the E. coli strains MG1655 (wildtype)and MG1655 (kdpA4, a kdpFABC-inactive mutant after a shift to K+ limitation.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
A method to compare kdpFABC expression between MG1655 (wildtype) and MG1655 (kdpA4) after a shift to K+ limitation, the RNA was extracted from samples taken at different points in time.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
Pulsed-FRAP measure the diffusion constants in confined volumes in small cells like E. coli and other bacteria or cellular organelles.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
A procedure to measure the levels of GSH and SLG before and after exposure to MG using formic acid. A similar expreimental set up as for potassium efflux experiments is used to which a silicon oil centrifugation step is incorporated. Samples are analysed by LC-MS-MS in order to quantify intracellular GSH and SLG levels.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
The reverse transcriptase synthesizes DNA, which complements the mRNA template.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
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
FRAP experiments are used for studying cytoplasmic diffusion in cells and cells membrane.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
Growing Escherichia coli to express KefF by adding IPTG for purification and kinetics experiments.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
Generating gene knock-ins using MJF618 expressing the defective lambdoid prophage recombination system λ red.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
Generating gene knock-outs using DY330 expressing the defective lambdoid prophage recombination system λ red.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
Experimental system that is designed to observe the in vivo stability and aggregation of a protein of interest.
Creator: Lisbeth Lyngberg
Submitter: Lisbeth Lyngberg
