Institute of Biochemistry and Technical Biochemistry

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41 to 50 of 66 Results

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...
NGS data related to Dossmann et al.: Specific DNMT3C flanking sequence preferences facilitate methylation of young murine retrotransposons 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...
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.
NGS data related to Rajaram et al.: Development of super-specific epigenome editing by targeted allele-specific DNA methylation 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...
Occurrence of expansins in the tree of life Apr 9, 2020 - Expansin Engineering Database Lohoff, Caroline, 2020, "Occurrence of expansins in the tree of life", https://doi.org/10.18419/darus-693, DaRUS, V1, UNF:6:eK0oQia4QiaiEO0m1BJFeA== [fileUNF] Comparison between expansins found in the Expansin Engineering Database (ExED) and literature.
Oxidation of ABTS by Trametes versicolor laccase Feb 15, 2022 - EnzymeML at work Ngubane, Sandile, 2022, "Oxidation of ABTS by Trametes versicolor laccase", https://doi.org/10.18419/darus-2467, DaRUS, V1 Investigated was the oxidation of ABTS and syringaldazine by Trametes versicolor laccase. For this, the concentration of the substrate over time was measured, for different initial concentrations. All measurements were repeated for three replicates.
PAZy(Universität Stuttgart) Nov 26, 2021Bioinformatics Supporting information and data for the PAZy database on plastics-active enzymes.
Profile hidden Markov model for PETase homologues Dec 1, 2021 - PAZy Buchholz, Patrick C. F., 2021, "Profile hidden Markov model for PETase homologues", https://doi.org/10.18419/darus-2055, DaRUS, V1, UNF:6:AEjnqfOrnimO5Q2xFDkQDw== [fileUNF] Sixteen protein sequences for enzymes with known activity against polyethylene terephthalate (PET) were clustered using CD-HIT to derive a reduced set of twelve centroid sequences. These twelve protein sequences were aligned in a structure-guided multiple sequence alignment by T-...
Profile hidden Markov models of the ExED Jan 30, 2020 - Expansin Engineering Database Lohoff, Caroline, 2020, "Profile hidden Markov models of the ExED", https://doi.org/10.18419/darus-623, DaRUS, V1 Profile hidden Markov models and their underlying multiple sequence alignments for the N- and C-terminal protein domains of expansins.
Profile hidden Markov models of the Glycoside Hydrolase 19 Engineering Database Jun 1, 2020 - Glycoside Hydrolase 19 Engineering Database Orlando, Marco, 2020, "Profile hidden Markov models of the Glycoside Hydrolase 19 Engineering Database", https://doi.org/10.18419/darus-803, DaRUS, V1 A starting alignment was built if other sequences with a known PDB structure were available, by performing a GH19 domain structure-based alignment generated through the mmaker command implemented in ChimeraX. Other seed sequences in the same superfamily were added to this fixed s...

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...

NGS data related to Dossmann et al.: Specific DNMT3C flanking sequence preferences facilitate methylation of young murine retrotransposons

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...

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.

NGS data related to Rajaram et al.: Development of super-specific epigenome editing by targeted allele-specific DNA methylation

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...

Occurrence of expansins in the tree of life

Apr 9, 2020 - Expansin Engineering Database

Lohoff, Caroline, 2020, "Occurrence of expansins in the tree of life", https://doi.org/10.18419/darus-693, DaRUS, V1, UNF:6:eK0oQia4QiaiEO0m1BJFeA== [fileUNF]

Comparison between expansins found in the Expansin Engineering Database (ExED) and literature.

Oxidation of ABTS by Trametes versicolor laccase

Feb 15, 2022 - EnzymeML at work

Ngubane, Sandile, 2022, "Oxidation of ABTS by Trametes versicolor laccase", https://doi.org/10.18419/darus-2467, DaRUS, V1

Investigated was the oxidation of ABTS and syringaldazine by Trametes versicolor laccase. For this, the concentration of the substrate over time was measured, for different initial concentrations. All measurements were repeated for three replicates.

PAZy(Universität Stuttgart)

Nov 26, 2021Bioinformatics

Supporting information and data for the PAZy database on plastics-active enzymes.

Profile hidden Markov model for PETase homologues

Dec 1, 2021 - PAZy

Buchholz, Patrick C. F., 2021, "Profile hidden Markov model for PETase homologues", https://doi.org/10.18419/darus-2055, DaRUS, V1, UNF:6:AEjnqfOrnimO5Q2xFDkQDw== [fileUNF]

Sixteen protein sequences for enzymes with known activity against polyethylene terephthalate (PET) were clustered using CD-HIT to derive a reduced set of twelve centroid sequences. These twelve protein sequences were aligned in a structure-guided multiple sequence alignment by T-...

Profile hidden Markov models of the ExED

Jan 30, 2020 - Expansin Engineering Database

Lohoff, Caroline, 2020, "Profile hidden Markov models of the ExED", https://doi.org/10.18419/darus-623, DaRUS, V1

Profile hidden Markov models and their underlying multiple sequence alignments for the N- and C-terminal protein domains of expansins.

Profile hidden Markov models of the Glycoside Hydrolase 19 Engineering Database

Jun 1, 2020 - Glycoside Hydrolase 19 Engineering Database

Orlando, Marco, 2020, "Profile hidden Markov models of the Glycoside Hydrolase 19 Engineering Database", https://doi.org/10.18419/darus-803, DaRUS, V1

A starting alignment was built if other sequences with a known PDB structure were available, by performing a GH19 domain structure-based alignment generated through the mmaker command implemented in ChimeraX. Other seed sequences in the same superfamily were added to this fixed s...

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