Data files

Zip-archive with induced fit docking results for methotrexate in its neutral and N1-protonated variant as individual ligand:receptor complex PDB files. The files are ordered as ranked by Glide docking scores. The hDHFR receptor was based on PDB-ID 1u72 without additional water molecules. Docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced Fit docking workflow (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Induced Fit Docking ...

Zip-archive with induced fit docking results for methotrexate in its neutral and N1-protonated variant as individual ligand:receptor complex PDB files. The files are ordered as ranked by Glide docking scores. The hDHFR receptor was based on PDB-ID 1u72 with explicit conserved structural water molecules. Docking results were obtained by Induced Fit docking with Schrödinger Glide and Prime in the Induced Fit docking workflow (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Induced ...

Compound SMILES of resynthesized or newly designed pteridine compounds 1b, 1c, 2a-e, 3a-e, 4a-j and 5a-f used for ligand preparation within Maestro (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, Maestro.). SMILES strings and compound identifiers are comma-separated and can be readily imported in Maestro.

Zip archive of N1 protonated reference and newly synthesized pteridines (series 1-5) in SDF format.

Pteridines checked for Pan-assay interference compounds with the FAF-Drugs4 webserver (https://fafdrugs4.rpbs.univ-paris-diderot.fr/, last checked August 2020 and Lagorce et al. (2015) Nucleic Acids Res. 43, W200–207). Archive of PAINS filtering and ADME-Tox prediction results from FAF-Drugs4 run performed April 2019 with compound SMILES as input: applied_filters.txt: list of filters used; compound.sdf, accepted.sdf, intermediate.sdf, rejected.sdf, covalent_inhibitors.sdf and pains.sdf: compound ...

Results of default run of Schrödinger QikProp (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, QikProp v4.6.) for reference pteridines (series 1) and newly synthesized N10-, PABA and tail-modified pteridines (series 2, 3 and 4). QikProp in silico predicts various physico-chemical compound properties and advanced descriptors related to administration, distribution, metabolism, excretion and toxicity of the compounds.

Results of default run of Schrödinger QikProp (Schrödinger, LLC, New York, NY, Schrödinger Release 2015-4, 2015, QikProp v4.6.) for newly synthesized compounds of the merged series (5a-5f). QikProp in silico predicts various physico-chemical compound properties and advanced descriptors related to administration, distribution, metabolism, excretion and toxicity of the compounds.

Raw data of the measurements obtained via DLS measurements. Can be opened with the Zetasizer software.

Semi-targeted Mass Spectrometry proteomics study to detect 12 selected proteins of two serum samples belonging to the FOLFOX-4 study on heavly-pretreated ovarian cancer patients. The two samples, F10 and F12, are basal samples collected at before the first FOLFOX-4 treatment cycle (T0) and were selected for this study because they show a different proteome profile.

Deatiled agenda forBest practices in research data management and stewardship (2021-06-14)

Previously identified gene targets were used as input (see miRNA gene target file).

Literature-curated transcription factor (TF) - miRNA pairs of deregulated miRNAs were extracted from TransmiR (Tong, Cui and Wang 2019 TransmiR). miRNA, target gene, and TF Interaction pairs were visualized in Cytoscape v3.8.2 (Shannon, P. et al. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research 13, 2498-2504, doi:Doi 10.1101/Gr.1239303 (2003). The missing ...

Previously identified gene targets were used as input (see miRNA gene target file).

Literature-curated transcription factor (TF) - miRNA pairs of deregulated miRNAs were extracted from TransmiR (Tong, Cui and Wang 2019 TransmiR). miRNA, target gene, and TF Interaction pairs were visualized in Cytoscape v3.8.2 (Shannon, P. et al. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research 13, 2498-2504, doi:Doi 10.1101/Gr.1239303 (2003). The missing ...

Identified gene targets of deregulated miRNAs were used as input. Ontology and pathway GO terms with an adjusted p-value < 0.05 were considered significantly overrepresented

identified gene targets were used as input on the gProfiler website. Ontology and pathway GO terms with an adjusted p-value <0.05 were considered significantly overrepresented.

We obtained PE associated microRNA based on previously mentioned experiments. miRTarBase v8.0 was used to identify gene targets and extract 1000 miRNA - gene pairs with 667 unique genes (Huang et al., 2020). miRTarBase is a database for experimentally validated miRNA-target interactions. To minimize false positives only strong-evidence miRNA-target pairs were considered.

We obtained PE associated microRNA based on previously mentioned experiments. miRTarBase v8.0 was used to identify gene targets and extract 1000 miRNA - gene pairs with 667 unique genes (Huang et al., 2020). miRTarBase is a database for experimentally validated miRNA-target interactions. To minimize false positives only strong-evidence miRNA-target pairs were considered.

The fasta file contains amino acid sequences of genes forming the accessory genome of the Clostridium beijerinckii species. As BLAST might experience some errors with repetitive sequences, here 76 sequences with a single kind of amino acid forming more than 25% of a sequence were discarded.

The fasta file contains amino acid sequences of unique genes found in various Clostridium beijerinckii strains.

The fasta file contains amino acid sequences of genes forming the accessory genome of the Clostridium beijerinckii species.

The fasta file contains amino acid sequences of genes forming the core genome of the Clostridium beijerinckii species.

Quantification of CPM and TCP concentrations in cod liver and bile using gas chromatography

Levels of cortisol+total protein and activities of cholinesterase, alanine aminotransferase (ALAT) and aspartate aminotransferase (ASAT) in plasma of cod exposed to chlorpyrifos-methyl

EROD activity in liver of cod exposed to chlorpyrifos-methyl

Overview of metabolomics results from liver of cod exposed to chlorpyrifos-methyl

Biometrics of IVN fish exposed to chlorpyrifos-methyl

Information connecting RNA seq fastq-files to corresponding fish ID/exposure regime

The four treatment groups were Control (0 mg CPM/kg, with DMSO), 0.5 mg CPM/kg, 4.2 mg CPM/kg and 23.2 mg CPM/kg. Each treatment group consisted of 9 fish. These fish were sampled from 3 different tanks per treatment, with n=9 per treatment. A total of 36 samples were sequenced. For each sample, about 50 million 150 bp paired-end reads were generated.

Master template for hands on session