1 to 10 of 70 Results
Jeltsch, Albert; Schnee, Philipp, 2025, "MD Simulations with PRDM9", https://doi.org/10.18419/DARUS-4567, DaRUS, V1
This data collection contains additional data related to Graf et al.: "Investigation and design of the dual specificity of the PRDM9 protein lysine methyltransferase". This includes: Modelled structures of PRDM9 bound to different peptides Source data of the results of the MD analysis MD simulations codes and analysis scripts |
Jeltsch, Albert; Bashtrykov, Pavel, 2025, "NGS data related to Sogl et al. "Specificities and flanking sequence preferences of bacterial DNA-(cytosine C5)-methyltransferases"", https://doi.org/10.18419/DARUS-4515, DaRUS, V1, UNF:6:bSvQoJxvb+T/iyQGPOvTBA== [fileUNF]
Analysis of flanking sequence preference with a randomized substrate and bioinformatic data For analysis of the flanking sequence preference, substrate with different target sites sites in a 9 or 10 bp randomized sequence context were prepared as described (Dukatz, et al. 2020; Dukatz, et al. 2022). Substrate methylation reactions were performed wi... |
Nov 27, 2024
Panzer, Tim, 2024, "Data related to Panzer: A Machine Learning Based Approach to Analyze Supersecondary Structures of Proteins", https://doi.org/10.18419/DARUS-4576, DaRUS, V1
This entry contains the data used to implement the bachelor thesis. It was investigated how embeddings can be used to analyze supersecondary structures. Abstract of the thesis: This thesis analyzes the behavior of supersecondary structures in the context of embeddings. For this purpose, data from the Protein Topology Graph Library was provided with... |
Aug 12, 2024 - Amplicon based bisulfite NGS data
Jeltsch, Albert; Bashtrykov, Pavel; Rajaram, Nivethika, 2024, "NGS data related to Rajaram et al.: Allele specific DNA demethylation ...", https://doi.org/10.18419/DARUS-4230, DaRUS, V2
Method overview To achieve targeted locus and allele-specific DNA demethylation, HEK293 cells were transfected with two plasmids. One plasmid contains, dCas9 fused to a SunTag with five repeats of the GCN4 peptide, separated by 22 aa long linkers, and scFv-fused TET1CD, as well as a GFP reporter protein. The other plasmid is a multiguide plasmid wi... |
Mar 28, 2024
Koeppl, Lars-Hendrik, 2024, "HPLC raw data related to Koeppl et al.: Structure, function and substrate preferences of archaeal S-adenosyl-L-homocysteine hydrolases", https://doi.org/10.18419/DARUS-4052, DaRUS, V1, UNF:6:WOWb9VZ7dRJmQmW8TZ5lMg== [fileUNF]
In this study, synthesis and cleavage reactions catalysed by S-adenosyl-L-homocysteine hydrolases originating from different domains of life were investigated. The reactions were studied using S-adenosyl-L-homocysteine or S-inosyl-L-homocysteine as substrate for the cleavage reaction, and L-homocysteine together with inosine or adenosine as substra... |
Jeltsch, Albert; Schnee, Philipp; Pleiss, Jürgen; Weirich, Sara, 2024, "Additional data related to Weirich et al.: Discovery of new NSD2 non-histone substrates and design of a super-substrate", https://doi.org/10.18419/DARUS-3815, DaRUS, V1
This data collection contains additional data related to Weirich et al.: "Discovery of new NSD2 non-histone substrates and design of a super-substrate". This includes Modelled structures of NSD2 bound to different peptides Source data of the results of the MD analysis MD simulations codes and analysis scripts |
Jeltsch, Albert; Bashtrykov, Pavel; Dossmann, Leonie; Emperle, Max, 2024, "NGS data related to Dossmann et al.: Specific DNMT3C flanking sequence preferences facilitate methylation of young murine retrotransposons", https://doi.org/10.18419/DARUS-3386, DaRUS, V1
Cloning and site-directed mutagenesis The gene of the catalytic, C-terminal domain of murine DNMT3C (amino acid residues 439-740 of P0DOY1) was obtained in E. coli codon optimized form from IDT Integrated DNA Technologies. The gene fragment was cloned with the StrataClone PCR Cloning Kit (Stratagene) into a StrataClone Vector Mix amp/kan (Stratagen... |
Jan 12, 2024 - Amplicon based bisulfite NGS data
Jeltsch, Albert; Bashtrykov, Pavel; Rajaram, Nivethika, 2023, "NGS data related to Rajaram et al.: Development of super-specific epigenome editing by targeted allele-specific DNA methylation", https://doi.org/10.18419/DARUS-3581, DaRUS, V2
Method overview To achieve targeted ASM, transient transfection of the dCas9-10X SunTag-BFP, scFv-DNMT3A-3L-sfGFP, and sgRNA-DsRed plasmids was performed in HEK293 cells. Control experiments were conducted with a scrambled sgRNA that does not have a binding site in the human genome. Initial studies showed that cells positive for all three plasmids... |
Jan 10, 2024 - Amplicon based bisulfite NGS data
Jeltsch, Albert; Bashtrykov, Pavel; Albrecht, Claudia, 2024, "NGS data related to Albrecht et al.: Locus specific and stable DNA demethylation at the H19/IGF2 ICR1 by epigenome editing using a dCas9-SunTag system and the catalytic domain of TET1", https://doi.org/10.18419/DARUS-3790, DaRUS, V1
Method overview For targeted DNA demethylation of the H19/IGF2 ICR1, HEK293 cells were transfected with two plasmids, one containing dCas9 fused to a SunTag with five repeats of the GCN4 peptide, separated by 22 aa long linkers, and scFv-fused TET1CD, as well as a GFP reporter protein. The second plasmid encodes five sgRNAs targeting the ICR1 and a... |
Jan 9, 2024
Häussler, Max, 2024, "Data for: 'EnzymeML-based modeling workflow: from raw data to kinetic parameters'", https://doi.org/10.18419/DARUS-3867, DaRUS, V1
Kinetic parameter estimates for small laccase (SLAC) catalyzed oxidation of ABTS, investigated across the temperature range between 25 °C and 45°C. This dataset contains the following files: Unprocessed absorption data from the respective enzyme assays (.txt) Derived calibration data for the respective calibration measurements (.json) EnzymeML Docu... |
