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1 to 10 of 12 Results
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....
GraphML files for sequence networks of PETases and PURases
Dec 1, 2021 - PAZy
Buchholz, Patrick C. F., 2021, "GraphML files for sequence networks of PETases and PURases", https://doi.org/10.18419/darus-2054, DaRUS, V1
The GraphML files contain the sequence networks and annotated metadata for protein sequences.
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-...
PAZy(Universität Stuttgart)
Nov 26, 2021Bioinformatics
Supporting information and data for the PAZy database on plastics-active enzymes.
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...
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...
EnzymeML(Universität Stuttgart)
Sep 16, 2021
The EnzymeML data repository of the Institute of Biochemistry and Technical Biochemistry.
Sequence cross-references and taxonomic lineage for glycoside hydrolase family 19
May 20, 2021 - Glycoside Hydrolase 19 Engineering Database
Buchholz, Patrick C. F., 2021, "Sequence cross-references and taxonomic lineage for glycoside hydrolase family 19", https://doi.org/10.18419/darus-1163, DaRUS, V1, UNF:6:zi8TRxkq1C/pCN14pXTA0Q== [fileUNF]
The Glycoside Hydrolase 19 Engineering Database (GH19ED) contains information on protein sequences and structures of glycoside hydrolases from family 19. This dataset lists cross-references to the National Center for Biotechnology Information (NCBI), cross-references to the Prote...
Consensus sequences of arylsulfatases and phosphonate monoester hydrolases
May 12, 2021 - Bioinformatics
Buchholz, Patrick C. F., 2021, "Consensus sequences of arylsulfatases and phosphonate monoester hydrolases", https://doi.org/10.18419/darus-1838, DaRUS, V1
A multiple sequence alignment was constructed by Clustal Omega for the 95 protein sequences annotated as homologues of arylsulfatases and the 85 protein sequences annotated as homologues of phosphonate monoester hydrolases, respectively. The HMMER software suite was used to deriv...
Protein sequences of arylsulfatases, phosphonate monoester hydrolases, and reconstructed ancestors
May 3, 2021 - Bioinformatics
Heberlein, Magdalena, 2021, "Protein sequences of arylsulfatases, phosphonate monoester hydrolases, and reconstructed ancestors", https://doi.org/10.18419/darus-1801, DaRUS, V1
Protein sequences were derived from a maximum-likelihood phylogenetic tree for arylsulfatases and phosphonate monoester hydrolases, including a selection of reconstructed ancestral sequences.
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