"LRRK2 kinase activity regulates lysosomal glucocerebrosidase in Parkinson's disease pathogenesis" Sequencing Data
Contributors: Daniel Ysselstein
... Sequencing of GBA1 (all exons) and LRRK2 (Exon 31 and 41) for all lines included in the manuscript: LRRK2 kinase activity regulates lysosomal glucocerebrosidase in Parkinson's disease pathogenesis. We do not observed unexpected point mutations in these genes in non-mutant cell lines.
Contributors: Ilias Georgakopoulos Soares
... The mechanisms that underpin how insertions or deletions (indels) become fixed in DNA have primarily been ascribed to replication-related and/or double-strand break (DSB)-related processes. We introduce a novel way to evaluate indels, orientating them relative to gene transcription. In so doing, we reveal a number of surprising findings: First, there is a transcriptional strand asymmetry in the distribution of mononucleotide repeat tracts in the reference human genome. Second, there is a strong transcriptional strand asymmetry of indels across 2,575 whole genome sequenced human cancers. We suggest that this is due to the activity of transcription-coupled nucleotide excision repair (TC-NER). Furthermore, TC-NER interacts with mismatch repair (MMR) under physiological conditions to produce strand bias. Finally, we show how insertions and deletions differ in their dependencies on these repair pathways. Our new analytical approach reveals new insights into the contribution of DNA repair towards indel mutagenesis in human cells.
Contributors: Juan_Gabriel Rueda-Bayona
... the folder contains input and setup files of the article An Alternative Method to Determine Extreme Hydrodynamic Forces with Data Limitations for Offshore Engineering
Top results from Data Repository sources. Show only results like these.
Data for: Species delimitation and evolutionary reconstruction within an integrative taxonomic framework: a case study on Rhinolophus macrotis complex (Chiroptera: Rhinolophidae)
Contributors: Keping Sun, Vu Dinh Thong, Kangkang Zhang, Jiang Feng, Hanbo Zhao, Lin Zhang, Tong Liu, YANYAN XIAO, Longru Jin, Gábor Csorba
... Raw data sets, including mitochondrial sequences, nuclear sequences, microsatellite data and GBS data used in this study.
Common genetic variations associated with the persistence of immunity following childhood immunisation
Contributors: Daniel O'Connor
... Genotyping data of common genetic variations associated with the persistence of immunity following childhood immunisation
Contributors: Esteban Finol Berrueta
... raw DENV genomic data for Finol E. & Ooi EE. Iscience submision
Contributors: Gil Sharon
... Raw data (excluding raw sequencing and metabolomic data) used to construct figures for manuscript. Data is predominantly in csv or tsv format. qza and qzv files are QIIME2 outputs and can be viewed at https://view.qiime2.org/ . mat files are mat lab datasets. Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice Gil Sharon1,*, Nikki Jamie Cruz1, Dae-Wook Kang2,3,21, Michael J. Gandal4,5,6,7, Bo Wang1, Young-Mo Kim8, Erika M. Zink8, Cameron P. Casey8, Bryn C. Taylor9, Christianne J. Lane10, Lisa M. Bramer11, Nancy G. Isern8, David W. Hoyt8, Cecilia Noecker12, Michael J. Sweredoski1, Annie Moradian1, Elhanan Borenstein12,13,14,15,16, Janet K. Jansson8, Rob Knight17,18,19, Thomas O. Metz8, Carlos Lois1, Daniel H. Geschwind4,5,6, Rosa Krajmalnik-Brown2,3, and Sarkis K. Mazmanian1,20,* Autism spectrum disorder (ASD) manifests as alterations in complex human behaviors including social communication and stereotypies. In addition to genetic risks, the gut microbiome differs between typically-developing (TD) and ASD individuals, though it remains unclear whether the microbiome contributes to symptoms. We transplanted gut microbiota from human donors with ASD and TD controls into germ-free mice, and reveal that colonization with ASD microbiota was sufficient to induce hallmark autistic behaviors. The brains of mice colonized with ASD microbiota display alternative splicing of ASD-relevant genes. Microbiome and metabolome profiles of mice harboring human microbiota predict that specific bacterial taxa and their metabolites modulate ASD behaviors. Indeed, treatment of an ASD mouse model with candidate microbial metabolites improves behavioral abnormalities and affects neuronal excitability in the brain. We propose that the gut microbiome modulates behaviors in mice via production of neuroactive metabolites, suggesting that gut-brain connections contribute to the pathophysiology of ASD.
Contributors: UnaElsLive Natra, mdgmatest5 live
... RDM - File Type Support 21May2019 ElsCustomer Apart from .u3d all files preview [ .obj / .ply / .vtk / .stl / .ent / .brk / .pdb / .pse / .mol / .mol2 / .cif / .u3d / .dcm / .nii] - .pse is not supported
Contributors: Yevgen Yurenko, Martin Lepšík, Juraj Dobiaš
... The dataset contains molecular dynamics trajectories of 300ns simulation of three complexes of Helidye1, a novel cationic helicene-like probe for DNA detection, with double-stranded DNA. In addition to trajectories, we add parameter files (mol2 and frc) for HeliDye1 containing atomic charges and parameter for dihedral and improper torsion angles.
Induction of Rare Conformation of Oligosaccharide by Binding to Calcium-dependent Bacterial Lectin: X-ray Crystallography and Modelling Study
Contributors: Martin Lepsik, Anne Imberty
... Parameters, inputs and trajectories for 600 ns molecular dynamics of Pseudomonas aeruginosa lectin LecB in complex with Lewis x tetrasaccharide using the most promising Setup4 (see the publication).