Asian endemicity and the 2013 Beach Soccer World Cup: two concealed faces of recent Zika virus expansion
Contributors: Quentin Le Hingrat
... In this deposit, the dataset used for our analysis and the sequences alignment are available. We also added the xml file which can be used to re-run the phylogenetic analyses or to extract the exact conditions of our analyses.
Data on the Mode of Interaction Between Bilberry Leaves Phenolic Compounds and 13S Buckwheat Globulin
Contributors: Varuzhan Sarkisyan, Yuliya Frolova, Nikita Petrov, Irina Vorobieva, Alla Kochetkova
... This data are related to the research paper entitled “Buckwheat Flour as a Matrix for Sorption of Plant Phenolics: Homology Modeling, Molecular Docking, and FTIR Study” . This data includes experimental procedures used to analyze the mode of binding between 13S Buckwheat globulin and phenolic compounds found in Buckwheat Leaves . Results of molecular docking study are presented in this dataset. References  V.A. Sarkisyan, Y. V. Frolova, N.A. Petrov, I.S. Vorobieva, A.A. Kochetkova, Buckwheat Flour as a Matrix for Sorption of Plant Phenolics: Homology Modeling, Molecular Docking, and FTIR Study, J. Mol. Graph. Model. in press (n.d.).  J. Hokkanen, S. Mattila, L. Jaakola, A.M. Pirttil, A. Tolonen, Identification of phenolic compounds from lingonberry (Vaccinium vitis-idaea L.), Bilberry (Vaccinium myrtillus L.) andHybrid Bilberry (Vaccinium x intermedium Ruthe L.) Leaves, J. Agric. Food Chem. 57 (2009) 9437–9447. doi:10.1021/jf9022542.
CRISPR/Cas9 deletions in a conserved exon of Distal-less generates gains and losses in a recently acquired morphological novelty in flies.
Contributors: Gowri rajaratnam
... This dataset contains the aligned fasta seqeuncing files used for characterising the CRISPR/Cas9 mutations in all mutants mentioned in the paper. It also contains the processed isoform sequencing files as well as the Mass Spectometry output for the protein sequencing experiment.
Data for: Anchored hybrid enrichment phylogenomics resolves the backbone of erebine moths (Lepidoptera: Noctuoidea)
Contributors: Nicholas Homziak, Marc Branham, Akito Kawahara, Jesse Breinholt, Caroline Storer
... Alignment used for ML analyses.
Contributors: michele mishto, Juliane Liepe, John Sidney, Alessandro Sette, Felix Lorenz
... Fig. 1 (+ 2D GR-LCL) files: filteredSearchResults.xlsx. Listed are all peptides identified in the HCT116, HCC1143 and 2D GR-LCL MHC-I immunopeptidomes (spliced and non-spliced, 9-12mer sequences) with MS/MS scan numbers, retention times, mass characteristics and ion scores. Fig. 1C-E File: LyS-tryp_HCC1143_30KDa.RAW LysC/trypsin digestion of the HCC1143 protein sample (proteins > 30kDa) measured by Q Exactive Orbitrap Fig. 3C Folder: HCC1143_mutation_cosmic_database Mutations of the HCC1143 cell line as reported in the Cosmic database (version 17/8/2016) files: Mutations_in_sampleWed Aug 17 16-37-54 2016.csv Mutations_in_sampleWed Aug 17 16-38-01 2016.csv Mutations_in_sampleWed Aug 17 16-38-09 2016.csv Mutations_in_sampleWed Aug 17 16-38-18 2016.csv Fig. 3C-E Folder: HCT116_mutation_cosmic_database Mutations of the HCT116 cell line as reported in the Cosmic database (version 17/8/2016) files: Mutations_in_sampleWed Aug 17 17-09-53 2016.csv Fig. S5 Folder: in_vitro_digestions files: RAW files of the in vitro digestions (with or without proteasome) of the synthetic polypeptides mutCHMP7 and mutRBBP7 (see Table S6) and the target synthetic peptides’ run. The MS/MS of the identified neoepitopes are shown in Fig. S5. In particular: - “synthetic_peptides.RAW” is a mix containing also the synthetic peptides CHMP7[A324T]_316-325 and RBBP7[N17D]_12-20 - “mutCHMP7_20h.RAW” is the digestion (20h) of the synthetic substrate mutCHMP7_312-330 with purified proteasome - “mutCHMP7_20h_no-proteasome.RAW” is the digestion (20h) of the synthetic substrate mutCHMP7_312-330 without purified proteasome - “mutRBBP7_20h.RAW” is the digestion (20h) of the synthetic substrate mutRBBP7_6-25 with purified proteasome - “mutRBBP7_20h_no-proteasome.RAW” is the digestion (20h) of the synthetic substrate mutRBBP7_6-25 without purified proteasome The scripts for the MHC-I spliced peptides’ database generation Folder: TourDeForce
The diversity, structure and function of heritable adaptive immunity sequences in the Aedes aegypti genome
Contributors: Zachary Whitfield
... Datasets associated with Whitfield, Dolan, Kunitomi et al., "The diversity, structure and function of heritable adaptive immunity sequences in the Aedes aegypti genome". See methods for description of individual files. Aag2_Contigs.fa is the fasta form of the analyzed genome with updated IDs more compatible with the uploaded bed files.
Contributors: Ewa Grochowska
... MSTN genotypes chromatograms
Data for: Quantifying fatigue overload retardation mechanisms by energy dispersive X-ray diffraction
Contributors: Chris Simpson, Pablo Lopez-Crespo, Philip J Withers, Shohei Kozuki, Thomas Connolley, Mahmoud Mostafavi
... The uploaded files contain the energy dispersive X-ray diffraction (EDXRD) data from experiment EE12205, carried out at the Diamond Light Source (I12:JEEP). The supplied files detail the crack tip strain fields at each load step ranging from Kmin to Kmax at six crack tip positions relative to the overload location. Measurements were made before, during and after the overload event at both (a) R = 0.1 and b) R = 0.4. File descriptions/meta data is given in file_list_EDXRD.csv. The data was processed using pyXe and can be read, re-analysed and plotted using the same software suite (https://github.com/casimp/pyxe).
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.