Contributors: Yee Fang Hum
... Unprocessed PacBio sequencing data files and barcode pairs used for each of the three mismatch repair mutant yeast strains. The DNA sequences of the recipient and donor alleles are provided as "recipient.txt" and "donor.txt", respectively. A complete list of the forward and reverse barcodes used in this study can be found in "Barcodes.txt".
Contributors: Gemma Owens
... Whole exome and transcriptome sequencing data for two patients with high-grade serous ovarian cancer. Data was used to identify non-synonymous somatic mutations which were predicted to give rise to neoantigens. Predicted neoantigens were filtered using peptide-MHC binding prediction algorithms. Neoantigens with a high predicted binding affinity were synthesised and screening for immunogenicity using autologous expanded TIL.
Contributors: Eveline Pinseel
... The data provide a concatenated alignment of the nuclear encoded 28S gene and the plastid rbcL of the diatom (Bacillariophyta) species complex Pinnularia borealis, including several Pinnularia taxa as outgroup. This dataset was used to built a phylogenetic tree to guide morphometric analysis of several cultures belonging to the P. borealis species complex.
Contributors: xianguang GUO
... Late Cenozoic stepwise aridification has transformed Central Asia into an arid environment, and the Pleistocene climatic oscillations exerted further ecological impact. Therefore, both aridification and glaciation would have considerably influenced the evolution of many midlatitude species in arid Central Asia (ACA). However, strong biotic evidence supporting this role is still lacking. We test this perspective using a phylogeographic study of Eremias velox, which is an arid-adapted lizard, across ACA using sequences from mitochondrial cytochrome b and 12S rRNA genes. This dataset comprises the novel cyt b and 12S rRNA gene sequences for 440 specimens of E. velox.
Extensive cryptic diversity in the terrestrial diatom Pinnularia borealis (Bacillariophyceae): concatenated alignment of 28S and rbcL
Contributors: Eveline Pinseel
... The dataset contains a fasta file with the concatenated sequences of 28S and rbcL of several members of the diatom genus Pinnularia (Pinnularia borealis in particular).
Programmed secretion arrest and receptor-triggered toxin export during antibacterial contact-dependent growth inhibition. Ruhe et al.
Contributors: Christoper S. Hayes
... Data for "Programmed secretion arrest and receptor-triggered toxin export during antibacterial contact-dependent growth inhibition (CDI)"
Contributors: Mathias Klok Pedersen
... MIRU-VNTR raw data used in software description article in PLOS ONE.
A comprehensive analysis of the faecal microbiome and metabolome of Strongyloides stercoralis infected volunteers from a non-endemic area
Contributors: Timothy Jenkins, Fabio Formenti, Cecilia Castro, Chiara Piubelli, Francesca Peradin, Dora Buonfrate, Domenico Otranto, Jules Griffin, Lutz Krause, Zeno Bisoffi
... In this study, we explore the impact of sole, natural infections by the human parasite Strongyloides stercoralis on the faecal gut microbiota and metabolic profiles of a cohort of human volunteers from northern Italy (S+), pre- and post-anthelmintic treatment, and compare the findings with data obtained from a cohort of uninfected controls from the same geographical area (S-). The collected data was obtained through high-throughput sequencing of bacterial 16S rRNA using an Illumina Miseq and nuclear magnetic resonance (NMR) and gas chromatography - mass spectrometry analyses of raw faecal samples. The data set includes four types of files: Raw joined read files - 1 per sample (demultiplexed): e.g. S+pre-treatment1.fasta OTU table created using Qiime including all of the taxonomic information: OTU_table.biom A table containing the metabolite quantification from the NMR and GC-MS analyses. These tables have been normalised to total area: Metabolomic_data_NMR_GC-MS_nomalised_to_total_area.xlsx Metadata file containing the relevant contextual information for each sample: Supplementary table S1.xlsx
Contributors: Ervin Fodor
... See Serna Martin et al Mol Cell 70, 1101-1110, 2018 for the description of data.
Contributors: Dr. Chitra Mandal, Devawati Dutta, Chhabinath Mandal
... We have conducted molecular dynamics simulations to obtain information about the structural aspects of sialylated glycans incorporated into the OprD protein. Four N-glycosylation sites on Asn196 (NLS), Asn218 (NYT), Asn251 (NTT) and Asn288 (NGS). Out of the four sites, Asn288 site is present in the extracellular loop region having high solvent accessibility, for its proper glycosylation. Molecular dynamic studies revealed that the core glycan moiety can properly fit into Asn288 with no spatial overlap for its proper glycosylation. Simulation of sialylated-glycan in free and conjugated states depicted that the population distribution of different conformers were in good agreement with the experimental structures. The permeability of the docked antibiotic into the OprD channel revealed its binding in loop2 region and interaction with a ladder of basic amino acids helps in traversing the channel. Furthermore, we demonstrated that sialylated-glycan core structure at Asn288 blocks the channel and hinders the antibiotic binding to loop2.