Project description:Raw images acquired with an Opera Phenix High-Content Screening System and using PRISM staining method. See "Multiplexed and high-througput neuronal fluorescence imaging with diffusable probes" Nature Comm (2018). Images are single plane single channel tiff files. file name indicates plate coordinates, field of view and plane. WO in file folder indicates washout round, where PRISM imaging probe was removed. Folder name indicates which PRISM target was imaged for that round. Baseline folder contains images before PRISM imaging probes were used. 4 channels per field. ch1: MAP2, ch2: DAPI, ch3:PRISM probe (indicated by folder name), ch4: vGlut.
Project description:Cardiac troponin T (cTnT) fragmentation in human serum was investigated using a newly developed targeted selected ion monitoring assay, as described in the accompanying article: "Development of a targeted selected ion monitoring assay for the elucidation of protease induced structural changes in cardiac troponin T" . This article presents data describing aspects of the validation and optimisation of this assay. The data consists of several figures, an excel file containing the results of a sequence identity search, and a description of the raw mass spectrometry (MS) data files, deposited in the ProteomeXchange repository with id PRIDE: PXD003187.
Project description:Efficient storage and retrieval of digital data is the focus of much commercial and academic attention. With personal computers, there are two main ways to retrieve files: hierarchical navigation and query-based search. In navigation, users move down their virtual folder hierarchy until they reach the folder in which the target item is stored. When searching, users first generate a query specifying some property of the target file (e.g., a word it contains), and then select the relevant file when the search engine returns a set of results. Despite advances in search technology, users prefer retrieving files using virtual folder navigation, rather than the more flexible query-based search. Using fMRI we provide an explanation for this phenomenon by demonstrating that folder navigation results in activation of the posterior limbic (including the retrosplenial cortex) and parahippocampal regions similar to that previously observed during real-world navigation in both animals and humans. In contrast, search activates the left inferior frontal gyrus, commonly observed in linguistic processing. We suggest that the preference for navigation may be due to the triggering of automatic object finding routines and lower dependence on linguistic processing. We conclude with suggestions for future computer systems design.
Project description:The Data described here provide the in depth proteomic assessment of the human dental pulp proteome and N-terminome (Eckhard et al., 2015) . A total of 9 human dental pulps were processed and analyzed by the positional proteomics technique TAILS (Terminal Amine Isotopic Labeling of Substrates) N-terminomics. 38 liquid chromatography tandem mass spectrometry (LC-MS/MS) datasets were collected and analyzed using four database search engines in combination with statistical downstream evaluation, to yield the by far largest proteomic and N-terminomic dataset of any dental tissue to date. The raw mass spectrometry data and the corresponding metadata have been deposited in ProteomeXchange with the PXD identifier <PXD002264>; Supplementary Tables described in this article are available via Mendeley Data (10.17632/555j3kk4sw.1).
Project description:We developed and validated ‘HIT-MAP’ (High-resolution Informatics Toolbox in MALDI-MSI Proteomics), an open-source bioinformatics workflow using peptide mass fingerprint analysis and a dual scoring system to computationally assign peptide and protein annotations to high mass resolution MSI datasets, and generate customisable spatial distribution maps. The uploaded files are an example dataset for the HiTMaP proteomics search engine, designed for MALDI-imaging proteomics annotation. The example data files contain one bovine lens tissue section and one mouse brain tissue section. The ID folder contains the protein/peptide identification result for each tissue segment, and the summary folder contains the protein cluster images.
Project description:The snail Bithynia siamensis goniomphalos acts as the first intermediate host for the human liver fluke Opisthorchis viverrini, the major cause of cholangiocarcinoma (CCA) in Northeast Thailand. This data article contains the results obtained from the analysis of the proteins differentially expressed in the snail B. siamensis goniomphalos upon infection with O. viverrini. It contains the data generated from iQuantitator software including a pdf of each sample with a protein?s relative expression summary and a per-protein detailed analysis of all time points studied and an excel file for each sample containing the raw data from iQuantitator analysis, including ID, mean, standard deviation, credible interval, log2 and description for every protein identified in each of the samples.
Project description:We used CyTOF to study CLL proliferation and its possible connections to MYC and mTOR pathway activities at single cell resolution. We measured the abundance of 33 proteins and phosphorylated proteins, including markers for cell type, cell proliferation and signaling pathway activity 16 in primary CLLs. We exposed the tumors to CpG ODN (5ug/mL), with the mTOR inhibitor everolimus (250 nM), with CpG ODN and everolimus combined, and DMSO control to elicit proliferation and assess its dependence on mTOR. The raw CyTOF data (.fcs files) are provided in a compressed folder "fcs_files.zip" and sample metadata are provided in "metaData.tsv" file.
Project description:SUMMARY:In cancer research, cell-based assays are used to assess cell migration and invasion. The major bottleneck is the lack of automated tools to visualize and analyse the large amounts of biological dose-response data produced. To address this challenge, we have developed an automated and free software package for dose-response analyses, DoRes, which is released as an add-on of the freely available and open-source tool CellMissy, dedicated to the management and analysis of cell migration data. DoRes implements non-linear curve fitting functionality into a robust, user-friendly and flexible software package with the possibility of importing a tabular file or starting from a cell migration experiment. We demonstrate the ability of the software by analysing public dose-response data and a typical cell migration experiment, and show that the extracted dose-response parameters and the calculated statistical values are consistently comparable to those of the widely used, commercial software GraphPad Prism. AVAILABILITY AND IMPLEMENTATION:The software here presented is a new module in CellMissy, an open-source and cross-platform package dedicated to the management, storage and analysis of cell migration data. The new module is written in Java, and inherits the cross-platform support from CellMissy. Source code and binaries are freely available under the Apache2 open-source licence at https://github.com/compomics/cellmissy/. SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.
Project description:Hereditary paroxysmal dyskinesias (PxD) are a heterogeneous group of movement disorders classified by frequency, duration, and triggers of the episodes. A young-adult onset canine PxD has segregated as an autosomal recessive trait in Soft-Coated Wheaten Terriers. The medical records and videos of episodes from 25 affected dogs were reviewed. The episodes of hyperkinesia and dystonia lasted from several minutes to several hours and could occur as often as >10/day. They were not associated with strenuous exercise or fasting but were sometimes triggered by excitement. The canine PxD phenotype most closely resembled paroxysmal non-kinesigenic dyskinesia (PNKD) of humans. Whole genome sequences were generated with DNA from 2 affected dogs and analyzed in comparison to 100 control canid whole genome sequences. The two whole genome sequences from dogs with PxD had a rare homozygous PIGN:c.398C > T transition, which predicted the substitution of an isoleucine for a highly conserved threonine in the encoded enzyme. All 25 PxD-affected dogs were PIGN:c.398T allele homozygotes, whereas there were no c.398T homozygotes among 1185 genotyped dogs without known histories of PxD. PIGN encodes an enzyme involved in the biosynthesis of glycosylphosphatidylinositol (GPI), which anchors a variety of proteins including CD59 to the cell surface. Flow cytometry of PIGN-knockout HEK239 cells expressing recombinant human PIGN with the c.398T variant showed reduced CD59 expression. Mutations in human PIGN have been associated with multiple congenital anomalies-hypotonia-seizures syndrome-1 (MCAHS1). Movement disorders can be a part of MCAHS1, but this is the first PxD associated with altered GPI anchor function.
Project description:We used phosphoproteomics to compare the responses of the ERK1/2 inhibitors, SCH772984 and GDC0994, and the MKK1/2 inhibitor, trametinib. These are compared with responses to the MKK1/2 inhibitor, selumetinib (AZD6244), previously measured by our lab in the same metastatic melanoma cell line. In three replicate experiments, we quantified a total of 12,805 class I phosphosites on 3,819 proteins in the trametinib-SCH772984-DMSO experiment, and 7,074 class I phosphosites on 2,453 in the GDC0994-SCH772984-DMSO experiment. This included 466 phosphosites that reproducibly decreased in response to at least one inhibitor in the trametinib-SCH772984-DMSO experiment and 414 phosphosites in the GDC0994-SCH772984-DMSO experiment. The results demonstrate linearity in signaling through the MAP kinase pathway. By comparing multiple inhibitors targeted to multiple tiers of protein kinases in the MAPK pathway, we gain insight into regulation and new targets of the oncogenic BRAF driver pathway in cancer cells, and a useful approach for evaluating the specificity of drugs and drug candidates. SILAC Experimental Design Experiment 1 Replicate 1: Heavy – DMSO, Medium – SCH772984, Light – Trametinib Replicate 2: Heavy – SCH772984, Medium – Trametinib, Light – DMSO Replicate 3: Heavy – Trametinib, Medium – DMSO, Light – SCH772984 SILAC Experimental Design Experiment 2 Replicate 1: Heavy – DMSO, Medium – SCH772984, Light – GDC0994 Replicate 2: Heavy – SCH772984, Medium – GDC0994, Light – DMSO Replicate 3: Heavy – GDC0994, Medium – DMSO, Light – SCH772984 File List 1. Zipped MaxQuant search results folder containing index and output folders for each raw file, ‘combined’ output folder, and mqpar.xml MaxQuant search parameters file 2. Individual raw files of phosphopeptide-enriched ERLIC fractions 3. Zipped MaxQuant version used for analysis 4. FASTA file containing Uniprot human identifications 5. Instructions for viewing annotated spectra