SOPs
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: Sahar Hassani, Inga Leena Angell, Jon Olav Vik, Graceline Tina Kirubakaran
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: Sahar Hassani, Inga Leena Angell, Jon Olav Vik, Graceline Tina Kirubakaran, Gareth Gillard, Arne Gjuvsland, Fabian Grammes, Hanne Hellerud Hansen, Thomas Harvey, Torgeir R. Hvidsten, Vitor Martins dos Santos, Dominic Nanton, Stuart Owen, Jacob Seilø Torgersen, Sandve Simen, Lars Snipen, Natalie Stanford, Kristil Sundsaasen, Kristina Vagonyte-Hallan, Dagmar Waltemath, Jesse van Dam, RAGNHILD ÅNESTAD
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
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