Analysis of Left Ventricular Profiles in Carfilzomib Treated and Control Mouse Specimens
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ABSTRACT: Wild-type C57BL/6N mice were treated with twice-weekly carfilzomib injections for a period of two weeks. Following this treatment, the left ventricular tissues were prepared for tmt-multiplexed mass spectrometry analysis to determine the protein-profiles of the treated hearts as opposed to those of untreated mouse specimens. For more experimental details and procedures, please see the attached methods file.
Project description:WT and mOCT1/2 knockout mice (FVB background) were treated with NaCl or Cisplatin (4 mg/kg bodyweight i.p.) for 4 weeks. The kidneys were perfused and analysed via nLC-MS/MS. Please see the respective manuscript for details.
Project description:To identify sites of ubiquitination in Myc-6His-Tagged forms of RAD23A and UBQLN1 for wild-type and forms with some arginine residues mutated to lysines (see FASTA file for details).
Project description:Raptor expression was specifically deleted in the tubular system of the kidney using an inducible Cre-Lox system under the control of a Pax8 promotor. Please see further details concerning the experimental procedures in the accompanied publication
Project description:Medicago truncatula endogenous small RNAs The dataset contains Medicago truncatula Gaertn. cv. Jemalong endogenous small RNA sequences in the range 18-28 nucleotides. High-throughput Solexa/Illumina sequencing was carried out at the Sainsbury Laboratory, Norwich, UK. Please see www.illumina.com for details of the technology. Small RNA sequences were mapped to Medicago truncatula genome release 2.0 (http://www.medicago.org/genome/), the number of matches to the unfinished genome, if any, is recorded in the Series supplementary file GSE13761_sequence_annotations.txt.gz.
Project description:Microarrays were used to identify genes that participate in the acid responce tolerance of C. jejuni. Three biological replicates of two different conditions (pH 5.5 and 7). Two slides and every slide contained three arrays- see attached additional file.
Project description:We developed a method that allows measuring the stable carbon isotope composition of individual species in microbial communities using metaproteomics. We call this methods “Direct Protein-SIF”. To benchmark this method, we measured twenty pure culture species using the Direct Protein-SIF method as well as Isotope Ratio Mass Spectrometry. Some of the pure cultures were measured in technical replicates to see how consistent Protein-SIF measurements are between mass spec runs. This submission thus contains 29 raw files for the pure cultures. See table in the submission for details of which species was measured for which .raw file. We also included the Direct Protein-SIF specific isotope pattern files as well as the .mzML files and PSM files required as input for the Direct Protein-SIF software. In addition to the pure culture a protein reference material (MKH files) was measured. The respective .raw files and isotopic pattern files are also included in this submission (see publication for details on how the reference material is used to calibrate the method).
Project description:High-throughput sequencing of individual olfactory sensory neurons from adult male mice.A multiplexed library of 72 single cells was prepared and purified using the Nextera XT DNA. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
Project description:Isolated murine kidney glomeruli were lysed in buffer containing 8M urea, and proteins were reduced and alkylated. Proteins were digested with trypsin. After reverse-phase chomatrography, peptides were fractionated using strong cation exchange chromatography. Phosphopeptides were enriched using IMAC (FeNTA) columns. Peptides were analyzed by LC-MS/MS on a Q Exactive mass spectrometer or an LTQ Orbitrap XL mass spectrometer. Metadata for Orbitrap samples (MaxQuant Output files include „Orbi“) 1. General features – 1.1 Global descriptors a. Responsible person or role: Markus Rinschen. markus.rinschen@uk-koeln.de; tobias.lamkemeyer@uni-koeln.de b. Instrument manufacturer, model: LTQ-Orbitrap XL, Thermo Scientific c. customization 2. Ion sources – ESI fed by nLC 2 (Proxeon) 3. Post source component 3.1. Analyser: MS1 survey scan in an Orbitrap and MS2 analysed in Linear Trap. 3.2. Activation/Dissociation: CID 4. Spectrum and peak list generation and annotation 4.1. Data acquisition: MaxQuant v. 1.3.05 Top one method with a cycle of one full MS1 scan in the Orbitrap, followed by the fragmentation with dynamic exclusion window of 60 seconds and followed by the acquisition of 5 product ion scans generated in the LTQ analyser, and detected in the LTQ. Unselected fragmentation. For further details, see .raw files. URL of file: Filename 4.2. Data analysis: MaxQuant v 1.3.05 Parameters used in the generation of peak lists or processed spectra: see annotation in “parameters” file. The mouse uniprot reference database “complete proteome” obtained on January 2nd, 2013 was used. Metadata for QExactive samples (Max Quant output files include „QE“) 1. General features – 1.1 Global descriptors a. Responsible person or role: Markus Rinschen. markus.rinschen@uk-koeln.de; Marcus Krüger marcus.krueger@mpi-bn.mpg.de b. Instrument manufacturer, model: Q Exactive Thermo Scientific c. customization 2. Ion sources – ESI fed by nLC 1000 (Proxeon) 3. Post source component 3.1. Analyser: MS1 survey scan in an Orbitrap and MS2 analysed in Orbitrap/HCD cell 3.2. Activation/Dissociation: HCD 4. Spectrum and peak list generation and annotation 4.1. Data acquisition: MaxQuant v. 1.3.05 Top one method with a cycle of one full MS1 scan in the Orbitrap, followed by the fragmentation with dynamic exclusion window of 20 seconds in the HCD cell and followed by the acquisition of 10 product ion scans generated in the LTQ analyser, and detected in the LTQ. Unselected fragmentation. For further details, see .raw files. URL of file: Filename 4.2. Data analysis: MaxQuant v 1.3.05 Parameters used in the generation of peak lists or processed spectra: see annotation in “parameters” file. The mouse uniprot reference database “complete proteome” obtained on January 2nd, 2013 was used.
Project description:Test dataset with example metadata and license file.
Non-commercial license is granted to use this data. Attribution is required. Please see the attached license file prior to using the data