1 to 10 of 21 Results
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 a... |
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... |
Apr 27, 2023 - Amplicon based bisulfite NGS data
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... |
Mar 14, 2023 - MD Simulations
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... |
Jan 10, 2023
Jeltsch, Albert; Broche, Julian, 2023, "Gene expression data related to Broche et al.: "Genome-wide deposition of 6-methyladenine in human DNA reduces the viability of HEK293 cells and directly influences gene expression"", https://doi.org/10.18419/darus-2813, DaRUS, V1
In the publication "Genome-wide deposition of 6-methyladenine in human DNA reduces the viability of HEK293 cells and directly influences gene expression" bacterial DNA-adenine N6-Methyltransferases were expressed in human HEK293 cells. Cell proliferation and gene expression were... |
Sep 27, 2022 - Amplicon based bisulfite NGS data
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. |
Aug 15, 2022 - MD Simulations
Jeltsch, Albert; Schnee, Philipp; Pleiss, Jürgen, 2022, "Additional data related to Schnee et al.: Mechanistic basis of the increased methylation activity of the SETD2 protein lysine methyltransferase towards a designed super-substrate peptide", https://doi.org/10.18419/darus-2508, DaRUS, V2
This data collection contains additional data related to Schnee et al.: Mechanistic basis of the increased methylation activity of the SETD2 protein lysine methyltransferase towards a designed super-substrate peptide. This includes MD simulations code and analysis scripts. The us... |