SOPs

SOP describing how to perform an ITC multiple injections experiment with a MicroCal PEAQ ITC by Malvern.

SOP describing how to perform an ITC (recurrent) single injections experiment with a MicroCal PEAQ ITC by Malvern.

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

...

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)

SOP describing how to perform Dynamic Light Scattering (DLS) measurements with Gre2p in cuvettes using a Zetasizer Nano DLS reader.

SOP describing the steps for use of the ITC device (MicroCal PEAQ ITC by Malvern).

SOP describing how to perform specific activity measurements with Gre2p in multiwell plates (96w) using an UV-Vis Plate reader (Synergy H1).

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:

./SewlyntestforS17.py

./tween/M1.csv

./tween/M2.csv

./tween/M3.csv

./tween/M4.csv

./treatments/M1.csv

./treatments/M2.csv

./treatments/M3.csv

...

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:

./ScriptforS13andS16.py

./ScriptforS20.py

and as input:

./SpAcdiffconditions.CSV

...

SOP describing how to perform activity measurements (inital rates) with Gre2p in multiwell plates (96w) using an UV-Vis Plate reader (Synergy H1).

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.

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.

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.

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.

This SOP describes the in silico ADME-Tox property prediction with QikProp for prepared pteridine ligands.

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.

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.

Instructions and details on the data analysis workflow.

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.

Aceton precipitation and protein digestion for proteomic workflow

SOP for bioleaching experiments carried out for microscopy analysis at UDE

steps conducted to pellet cells for RNA and protein extraction

This file describes the naming system used to uniquely identify samples

SOP for extracting DNA, RNA and Proteins from the mineral pellet of a bioleaching culture using hot acidic phenol.

Current draft.

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.

sampling procedure for mineral containing leaching experiments