Contributors: Jeny Bastida, Alejandro Crampet, Melitta Meneghel, Victor Morais
... This dataset correspond to the proteomic analysis of the article entitle “Preliminary Biochemical and Venomic Characterization of the Venom of Phalotris lemniscatus (Serpentes, Colubridae)” sending to Current topics in medicinal chemistry. The data set include the raw files of each band of mass spectroscopy and the database used to identify the proteins. To observe the SDS page, please refer to the article. “Protein bands were excised and sent to the Spectroscopy and Biophysics Core, University of Nebraska, Lincoln (via Science Exchange) to in-gel trypsin digestion and peptide fragmentation by LC-MS/MS. The instrument was an LTQ Velos Pro (Thermo Scientific) equipped with dual pressure ion-trap. Raw data obtained by proteomic analysis was analyzed using MaxQuant software [30–32] with the default parameters (false discovery rate 0,01). As a sequence database to match for protein identification, a fasta file download from Uniprot was used. Database was constituted by all the reviewed sequenced proteins of snakes, around 2500 proteins from Swiss-Prot database (taxonomy:"Serpentes (snakes) " AND reviewed:yes)”.
Contributors: Esteban Finol Berrueta
... raw DENV genomic data for Finol E. & Ooi EE. Iscience submision
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
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Data for: SUBDUCTION CONTROL ON THE CURIE ISOTHERM AROUND THE PACIFIC-NORTH AMERICA PLATE BOUNDARY IN NORTHWESTERN MEXICO (GULF OF CALIFORNIA). PRELIMINARY RESULTS.
Contributors: Oscar Campos Enriquez, erdinc oksum, Juan-Manuel Espinosa-Cardeña
... This repository contains the raw data necesay to reproduce our results. In particular, data necesary to reproduce the results shown in Figures 5a,5b, %fc, 6a, 6b, 6c, and 7a, and 7b are included, as well as instructions how to reproduce our results.
Supplementary Data S1: Next generation sequencing from Hepatozoon canis (Apicomplexa: Coccidia: Adeleorina): Complete apicoplast genome and multiple mitochondrion-associated sequences
Contributors: Alexandre Léveillé, John Barta
... These files comprise all of the NGS sequence assemblies referred to in the article: "Next generation sequencing from Hepatozoon canis (Apicomplexa: Coccidia: Adeleorina): Complete apicoplast genome and multiple mitochondrion-associated sequences." All assemblies were generated from Illumina HiSeq 2500 sequencing data (126 bp paired-end reads, insert length ~500 bp). In the case of mitochondrion-associated sequences 1, 2, 3 and 4: PCR and Sanger sequencing data were utilized to provide additional assembly coverage of CDS regions. Files included are: BAM assembly files: .bam, .bai and .fasta (these files are needed together to generate a BAM assembly flat file - supported by many software platforms). Geneious assembly files: Complete annotated assemblies (with NGS read pairings) can be viewed with Geneious software (versions 6.1 or newer). These files will provide the greatest details of the assembly data. Jpeg images of Geneious assemblies: These files were provided for ease of viewing and rapid analysis. Note: images were not generated for the complete ribosomal DNA unit and 18S rDNA variant assemblies as these assemblies were too large to viewed as images.
Essential gene profiles for human pluripotent stem cells identify uncharacterized genes and substrate dependencies. Mair et al.
Contributors: Barbara Mair, Jelena Tomic, Sanna Masud, Jason Moffat
... Human pluripotent stem cells (hPSCs) provide an invaluable tool for modeling diseases and hold promise for regenerative medicine. For understanding pluripotency and lineage differentiation mechanisms, a critical first step involves systematically cataloging genes that are indispensable for hPSC maintenance and proliferation. To map genetic determinants of hPSC fitness, we performed genome-scale loss-of-function screens in an inducible Cas9 H1 hPSC line cultured on feeder cells and feeder-free to identify essential genes. Among these, we found FOXH1 and VENTX, genes that encode transcription factors previously implicated in stem cell biology, as well as an uncharacterized gene, C22orf43/DRICH1. hPSCs essential genes are substantially different from other cell lines, and gene essentiality in hPSCs is highly context-dependent with respect to different growth substrates. Our CRISPR screens establish parameters for genome-wide screens in hPSCs, which will facilitate the characterization of unappreciated regulators of hPSC biology to understand the genetic wiring of hPSC fitness and pluripotency.
Contributors: M. Florencia Martini
... Files of DMPC-melittin and DMPC-pentalysin interaction, and different types of data analysis
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
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: 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.