Department of Molecular Biochemistry

Featured Dataverses

In order to use this feature you must have at least one published or linked dataverse.

Publish Dataverse

Are you sure you want to publish your dataverse? Once you do so it must remain published.

Publish Dataverse

This dataverse cannot be published because the dataverse it is in has not been published.

Delete Dataverse

Are you sure you want to delete your dataverse? You cannot undelete this dataverse.

11 to 20 of 25 Results

Additional data related to Khella et al.: The T1150A cancer mutant of the protein lysine methyltransferase NSD2 can introduce H3K36 trimethylation 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 peptide complex Modelled structures of NSD2 bound to different peptides and...
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" 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 investigated. Gene expression was investigated by RNA-seq. RNA-seq dat...
NGS data related to Dukatz et al.: DNA methyltransferase DNMT3A forms interaction networks with the CpG site and flanking sequence elements for efficient methylation 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.
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 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 usage of these Phyton scripts is further explained in the enclosed readm...
Python scripts related to MD simulations in "Preferential interaction of DNMT3A subunits containing the R882H cancer mutation leads to dominant changes of flanking sequence effects" Feb 1, 2022 - MD Simulations Jeltsch, Albert; Schnee, Philipp; Pleiss, Jürgen, 2022, "Python scripts related to MD simulations in "Preferential interaction of DNMT3A subunits containing the R882H cancer mutation leads to dominant changes of flanking sequence effects"", https://doi.org/10.18419/DARUS-2463, DaRUS, V1 Python scripts used for the Molecular Dynamics Simulation presented in "Preferential interaction of DNMT3A subunits containing the R882H cancer mutation leads to dominant changes of flanking sequence effects"
MD Simulations(Universität Stuttgart) Jan 31, 2022
Deep enzymology data related to Adam et al.: Flanking sequences influence the activity of TET1 and TET2 methylcytosine dioxygenases and affect genomic 5hmC patterns Dec 17, 2021 - Amplicon based bisulfite NGS data 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. Briefly, the following single-stranded oligonucleotides containing a...
NGS data related to Bröhm et al.: Methylation of recombinant mononucleosomes by DNMT3A demonstrates efficient linker DNA methylation and a role of H3K36me3 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 remove residual unbound DNA. Afterwards, DNMT3A2 or DNMT3AC was added to...
Data related to "Preferential interaction of DNMT3A subunits containing the R882H cancer mutation leads to dominant changes of flanking sequence effects" Nov 11, 2021 - Amplicon based bisulfite NGS data 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 universal primer. The obtained library of double-stranded DNA oligonucleot...
Data related to "Structural and biochemical insight into the mechanism of dual CpG site binding and methylation by DNMT3A" Apr 12, 2021 - Amplicon based bisulfite NGS data Jeltsch, Albert; Bashtrykov, Pavel; Adam, Sabrina; Kunert, Stefan, 2021, "Data related to "Structural and biochemical insight into the mechanism of dual CpG site binding and methylation by DNMT3A"", https://doi.org/10.18419/DARUS-1781, DaRUS, V1 Methylation of substrate libraries Single-stranded DNA oligonucleotides used for generation of double stranded substrates with different distance between CpG sites were obtained from IDT. Sixteen single-stranded oligonucleotides were pooled in equimolar amounts and the second strand synthesis was conducted by a primer extension reaction using one u...

Additional data related to Khella et al.: The T1150A cancer mutant of the protein lysine methyltransferase NSD2 can introduce H3K36 trimethylation

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 peptide complex Modelled structures of NSD2 bound to different peptides and...

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"

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 investigated. Gene expression was investigated by RNA-seq. RNA-seq dat...

NGS data related to Dukatz et al.: DNA methyltransferase DNMT3A forms interaction networks with the CpG site and flanking sequence elements for efficient methylation

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.

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

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 usage of these Phyton scripts is further explained in the enclosed readm...

Python scripts related to MD simulations in "Preferential interaction of DNMT3A subunits containing the R882H cancer mutation leads to dominant changes of flanking sequence effects"

Feb 1, 2022 - MD Simulations

Jeltsch, Albert; Schnee, Philipp; Pleiss, Jürgen, 2022, "Python scripts related to MD simulations in "Preferential interaction of DNMT3A subunits containing the R882H cancer mutation leads to dominant changes of flanking sequence effects"", https://doi.org/10.18419/DARUS-2463, DaRUS, V1

Python scripts used for the Molecular Dynamics Simulation presented in "Preferential interaction of DNMT3A subunits containing the R882H cancer mutation leads to dominant changes of flanking sequence effects"

MD Simulations(Universität Stuttgart)

Jan 31, 2022

Deep enzymology data related to Adam et al.: Flanking sequences influence the activity of TET1 and TET2 methylcytosine dioxygenases and affect genomic 5hmC patterns

Dec 17, 2021 - Amplicon based bisulfite NGS data

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. Briefly, the following single-stranded oligonucleotides containing a...

NGS data related to Bröhm et al.: Methylation of recombinant mononucleosomes by DNMT3A demonstrates efficient linker DNA methylation and a role of H3K36me3

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 remove residual unbound DNA. Afterwards, DNMT3A2 or DNMT3AC was added to...

Data related to "Preferential interaction of DNMT3A subunits containing the R882H cancer mutation leads to dominant changes of flanking sequence effects"

Nov 11, 2021 - Amplicon based bisulfite NGS data

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 universal primer. The obtained library of double-stranded DNA oligonucleot...

Data related to "Structural and biochemical insight into the mechanism of dual CpG site binding and methylation by DNMT3A"

Apr 12, 2021 - Amplicon based bisulfite NGS data

Jeltsch, Albert; Bashtrykov, Pavel; Adam, Sabrina; Kunert, Stefan, 2021, "Data related to "Structural and biochemical insight into the mechanism of dual CpG site binding and methylation by DNMT3A"", https://doi.org/10.18419/DARUS-1781, DaRUS, V1

Methylation of substrate libraries Single-stranded DNA oligonucleotides used for generation of double stranded substrates with different distance between CpG sites were obtained from IDT. Sixteen single-stranded oligonucleotides were pooled in equimolar amounts and the second strand synthesis was conducted by a primer extension reaction using one u...

Add Data

Share Dataverse

Link Dataverse

Reset Modifications