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1 to 10 of 20 Results
Amplicon based bisulfite NGS data(Universität Stuttgart)
Jan 29, 2020
Deep enzymology data related to Adam et al.: DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation
Deep enzymology data related to Adam et al.: DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation
Jan 30, 2020 - Amplicon based bisulfite NGS data
Jeltsch, Albert; Bashtrykov, Pavel; Adam, Sabrina, 2020, "Deep enzymology data related to Adam et al.: DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation", https://doi.org/10.18419/darus-628, DaRUS, V1
Methylation of random flank substrates: Libraries of double stranded DNA substrates with unmethylated or hemimethylated CpG sites in randomized sequence context were methlyated by DNMT1. Reactions were stopped by shock freezing in liquid nitrogen, then treated with proteinase K f...
Deep enzymology data related to Adam et al.: DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation
Deep enzymology data related to Adam et al.: DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation
Jan 30, 2020 - Amplicon based bisulfite NGS data
Jeltsch, Albert; Bashtrykov, Pavel; Adam, Sabrina, 2020, "Deep enzymology data related to Adam et al.: DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation", https://doi.org/10.18419/darus-629, DaRUS, V1
Methylation of long hemimethylated DNA substrates: Methylation of the 349 bp long hemimethylated substrate with DNMT1 was carried out in 1X methylation buffer (100 mM HEPES, 1 mM EDTA, 0.5 mM DTT, 0.1 mg/mL BSA, pH 7.2 with KOH) in the presence of 1 mM AdoMet. For the methylation...
Deep enzymology data related to Gao et al.: Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms
Deep enzymology data related to Gao et al.: Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms
Jan 30, 2020 - Amplicon based bisulfite NGS data
Jeltsch, Albert; Bashtrykov, Pavel; Emperle, Max; Adam, Sabrina; Dukatz, Michael, 2020, "Deep enzymology data related to Gao et al.: Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms", https://doi.org/10.18419/darus-627, DaRUS, V1
Experimental procedures: Libraries of double stranded DNA substrates with CpG, CpH or CpN sites in randomized sequence context were methlyated by DNMT3A or DNMT3B. Reactions were stopped by shock freezing in liquid nitrogen, then treated with proteinase K for 2 hours. Afterwards,...
Deep enzymology data related to Dukatz et al.: Complex DNA sequence readout mechanisms of the DNMT3B DNA methyltransferase.
Deep enzymology data related to Dukatz et al.: Complex DNA sequence readout mechanisms of the DNMT3B DNA methyltransferase.
Sep 1, 2020 - Amplicon based bisulfite NGS data
Jeltsch, Albert; Bashtrykov, Pavel; Dukatz, Michael; Adam, Sabrina, 2020, "Deep enzymology data related to Dukatz et al.: Complex DNA sequence readout mechanisms of the DNMT3B DNA methyltransferase.", https://doi.org/10.18419/darus-815, DaRUS, V3
Experimental procedures: Libraries of double stranded DNA substrates with CpG, CpH or CpN sites in randomized sequence context were methlyated by DNMT3B. Reactions were stopped by shock freezing in liquid nitrogen, then treated with proteinase K for 2 hours. Afterwards, the DNA w...
Data related to "Structural and biochemical insight into the mechanism of dual CpG site binding and methylation by DNMT3A"
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 str...
Data related to "Preferential interaction of DNMT3A subunits containing the R882H cancer mutation leads to dominant changes of flanking sequence effects"
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 univ...
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 rem...
Deep enzymology data related to Adam et al.: Flanking sequences influence the activity of TET1 and TET2 methylcytosine dioxygenases and affect genomic 5hmC patterns
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....
MD Simulations(Universität Stuttgart)
Jan 31, 2022
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