1 to 10 of 15 Results
Mar 28, 2024 - MD Simulations
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 simulati... |
Mar 4, 2024 - Amplicon based bisulfite NGS data
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 Clo... |
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 geno... |
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 pr... |
Jeltsch, Albert; Bashtrykov, Pavel; Adam, Sabrina, 2023, "NGS data related to Adam et al.: On the accuracy of the epigenetic copy machine - comprehensive specificity analysis of the DNMT1 DNA methyltransferase", https://doi.org/10.18419/darus-3334, DaRUS, V2, UNF:6:ERMvcNuV8nq+mI9Q5Xu53A== [fileUNF]
Expression and purification of DNMT1 for biochemical work Full length murine DNMT1 (UniProtKB P13864) was overexpressed and purified as described (Adam, et al. 2020) using the Bac-to-Bac baculovirus expression system (Invitrogen). The expression construct of the DNMT1 with mutate... |
Jeltsch, Albert; Schnee, Philipp; Saad, Mina; Weirich, Sara; Pleiss, Jürgen; Bashtrykov, Pavel, 2023, "Additional data related to Khella et al.: The T1150A cancer mutant of the protein lysine methyltransferase NSD2 can introduce H3K36 trimethylation", https://doi.org/10.18419/darus-3263, DaRUS, V1
This data collection contains additional data related to Khella et al.: "The T1150A cancer mutant of the protein lysine methyltransferase NSD2 can introduce H3K36 trimethylation". This includes Movie 1: Example of a successful docking of AdoMet to the NSD2 T1150A - H3K36me2 pepti... |
Jeltsch, Albert; Bashtrykov, Pavel; Dukatz, Michael; Adam, Sabrina, 2022, "NGS data related to Dukatz et al.: DNA methyltransferase DNMT3A forms interaction networks with the CpG site and flanking sequence elements for efficient methylation", https://doi.org/10.18419/darus-2993, DaRUS, V1
The naming of the files is described in the Supplemental Tables 1 of the accompanying manuscript. |
Jeltsch, Albert; Bashtrykov, Pavel; Adam, Sabrina, 2021, "Deep enzymology data related to Adam et al.: Flanking sequences influence the activity of TET1 and TET2 methylcytosine dioxygenases and affect genomic 5hmC patterns", https://doi.org/10.18419/darus-2114, DaRUS, V2
Experimental procedures for deep enzymology reactions with randomized substrates: For analysis of flanking sequence preferences of the TET enzymes, a similar approach as described for DNMTs (Emperle et al., 2019; Gao et al., 2020; Adam et al., 2020; Dukatz et al., 2020) was used.... |
Nov 25, 2021 - Amplicon based bisulfite NGS data
Jeltsch, Albert; Bashtrykov, Pavel; Bröhm, Alexander; Dukatz, Michael; Adam, Sabrina, 2021, "NGS data related to Bröhm et al.: Methylation of recombinant mononucleosomes by DNMT3A demonstrates efficient linker DNA methylation and a role of H3K36me3", https://doi.org/10.18419/darus-1252, DaRUS, V2
Methylation experiments: For the competitive nucleosome methylation experiments, 0.6 pmol of each nucleosome variant were digested with MluI (NEB) for 60 min at 37°C in 10 µL NEB Cutsmart buffer (50 mM KOAc/20 mM Tris-acetate pH 7.9, 10 mM Magnesium Acetate, 100 µg/mL BSA) to rem... |
Jeltsch, Albert; Bashtrykov, Pavel; Adam, Sabrina; Mack, Alexandra; Emperle, Max, 2021, "Data related to "Preferential interaction of DNMT3A subunits containing the R882H cancer mutation leads to dominant changes of flanking sequence effects"", https://doi.org/10.18419/darus-2231, DaRUS, V1
Methylation of substrate libraries Single-stranded DNA oligonucleotides used for generation of double stranded substrates with a distance of 12 base pairs between CpG sites were obtained from IDT. Second strand synthesis was conducted by a primer extension reaction using one univ... |
