ABSTRACT: PXD ID: PXD000104. Origina data file: v120523v04.mgf. Proteomic analysis of chick vestibualr hair bundles purified using the twist-off method.
Project description:This dataset was created to (i) compare the protein expression of E. coli DSM613 cells infected and uninfected with phage vB_EcoS-EE09 and (ii) detect structural proteins of phage vB_EcoS-EE09. Thus, this set provides proteomic data of three setups: 1. Uninfected E. coli DSM613 (file names [file ID]: 04_22A [F40]; 13_ecolicontrol_01 [F13]; 14_ecolicontrol_02 [F14]) 2. E. coli DSM613 infected with phage vB_EcoS-EE09 (file names [file ID]: 02_13A [F39]; 27_ecoliinfected_01 [F27]; 28_ecoliinfected_02 [F28]) 3. Cell-free phage lysate of phage vB_EcoS-EE09 (sample name: 01_EE09)
Project description:Reproductive performance of female pigs that do not receive sufficient colostrum from birth is permanently impaired. Whether lactocrine deficiency, reflected by low serum immunoglobulin immunocrit (iCrit), affects patterns of endometrial gene expression during the periattachment period of early pregnancy is unknown. Here, objectives were to determine effects of low iCrit at birth on the adult endometrial transcriptome on pregnancy day (PxD) 13. On the first day of postnatal life, gilts were assigned to high or low iCrit groups. Adult high (n = 8) and low (n = 7) iCrit gilts were bred (PxD 0), humanely slaughtered on PxD 13 when tissues and fluids were collected. The endometrial transcriptome was defined for each group using mRNAseq and microRNAseq. Reads were mapped to the Sus scrofa 11.1 genome build. Mature microRNAs were annotated using miRBase 21. Differential expression was defined based on fold change (≥ ± 1.5). Lactocrine deficiency did not affect corpora lutea number, uterine horn length, uterine wet weight, conceptus recovery, or uterine luminal fluid estrogen content on PxD 13. However, mRNAseq revealed 1157 differentially expressed endometrial mRNAs in high versus low iCrit gilts. Differentially expressed genes had functions related to solute transport, endometrial receptivity, and immune response. Six differentially expressed endometrial microRNAs included five predicted to target 62 differentially expressed mRNAs, affecting similar biological processes. Thus, lactocrine deficiency on the first day of postnatal life can alter uterine developmental trajectory with lasting effects on endometrial responses to pregnancy as reflected at the level of the transcriptome on PxD 13.
Project description:Total pancreatic RNA was isolated from 3 week old NOD.scid, NOD, BDC2.5/NOD and BDC2.5/NOD.scid animals by GITC method. Targets were produced using standard Affymetrix procedures from about 10ug total RNA. The data from NOD.scid, NOD, BDC2.5/NOD and BDC2.5/NOD.scid Affymetrix MGU74Av2 cel files was converted into Robust Multi Array (RMA) text file for analysis using GeneSpring 6.1 Keywords: other
Project description:These are the tiling array data for the experiments describing LADs on murine chromosomes 5, 12, and 15 by Dam-ID, as determined by LMNB and EMD Dam tagging and detection experiments Supplemental Bed file contains GADA algorithm calls for genomic regions of chromosomes 5, 12 and 15 (-1= no lad, high confidence, 0=indeterminate, 1=LAD, high confidence)
Project description:We performed an extensive qualitative characterization of the platelet granule proteome using subcellular fractionation followed by mass spectrometry analysis and functional annotation. Platelets were isolated from whole blood by centrifugation and their level of purity was tested by microscopic inspection, western blot and Leucocount kit. Subcellular fractionation based on sucrose gradient was used to enrich sample in secretory granules. Then sample quality was assessed by western blot and electronic microscopy, prior proteomic study. Samples were trypsin digested and analyzed using an Orbitrap Velos in a gas-phase fractionation mode. The m/z ranges for the selection of precursor ions were 400-521, 516-690, 685-986 and 963-2000 Thomsons. The 2 technical replicates were analyzed by a GPF series of injections. Protein identification was performed using the EasyProt resource. The module EasyProtConv was used to generate the MGF file from the raw data. The peaklist files were searched against the UniProt database (2011_02 of 08-Feb-2011) using EasyProt. Eight-hundred-and-twenty-seven proteins were identified, most of them being associated to granules and to the granule’s secretory machinery.
Project description:<p>The effects of iron deficiency (ID) during infancy extend beyond the hematologic compartment and include short- and long-term adverse effects on many tissues including the brain. However, sensitive biomarkers of iron-dependent brain health are lacking in humans. To determine whether serum and cerebrospinal fluid (CSF) biomarkers of ID-induced metabolic dysfunction are concordant in the pre/early anemic stage of ID before anemia in a nonhuman primate model of infantile iron deficiency anemia (IDA). ID (n = 7), rhesus infants at 4 mo (pre-anemic period) and 6 mo of age (anemic) were examined. Hematological, metabolomic and proteomic profiles were generated via HPLC/MS at both time points to discriminate serum biomarkers of ID-induced brain metabolic dysfunction. We identified 227 metabolites and 205 proteins in serum. Abnormalities indicating altered liver function, lipid dysregulation and increased acute phase reactants were present in ID. In CSF, we measured 210 metabolites and 1560 proteins with changes in ID infants indicative of metabolomic and proteomic differences indexing disrupted synaptogenesis. Systemic and CSF proteomic and metabolomic changes were present and concurrent in the pre-anemic and anemic periods. Multiomic serum and CSF profiling uncovered pathways disrupted by ID in both the pre-anemic and anemic stages of infantile IDA, including evidence for hepatic dysfunction and activation of acute phase response. Parallel changes observed in serum and CSF potentially provide measurable serum biomarkers of ID that reflect at-risk brain processes prior to progression to clinical anemia.</p><p><br></p><p><strong>Data availability:</strong></p><p>The proteomics data have been deposited into the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier <a href='https://www.ebi.ac.uk/pride/archive/projects/PXD028275' rel='noopener noreferrer' target='_blank'>PXD028275</a>.</p>
Project description:MO3.13 is an immortal human-human hybrid cell line that express phenotypic characteristics of primary oligodendrocytes. It was created by fusing a 6-thioguanine-resistant mutant of the human rhabdomyosarcoma RD (cancer of skeletal muscle) with adult human oligodendrocytes by a lectin-enhanced polyethylene glycol procedure. In contrast to the tumor parent, MO3.13 expressed surface immunoreactivity for galactosyl cerebroside(GS) and intracellular immunoreactivity for myelin basic protein (MBP), proteolipid protein (PLP), and glial fibrillary acidic protein (GFAP). MO3.13 also exhibit the markers of immature oligodendrocytes GalC (galactosylceramidase) and CNPase. Upon differentiation, the MO3.13 cells have been also shown to express the MBP and MOG markers. Data analysis: Each MS raw file was processed using ProteoWizard for the generation of a MGF file. These were processed in SearchGUI, which runs the search engines Open Mass Spectrometry Search Algorithm (OMSSA) and X!Tandem against the UniProt human protein database (release 2013_08, 20,266 sequences). Search parameters were: peptide and fragment ion mass accuracy 10 ppm and 0.5 Da, respectively; protein and peptide FDRs 1%; two miss cleavages; trypsin as enzyme; fixed modifications: cysteine carbamidomethylation; variable modifications: methionine oxidation. In order to generate one single proteome dataset of MO3.13, resulting data was processed in PeptideShaker.
Project description:Twenty million LbetaT2 cells were transfected with either control or Galphas siRNA, then were seeded in 100-mm cell culture plates in DMEM + 10% FBS. Two days later, cells were washed twice with pre-warmed PBS. Conditioned media was harvested another 24 h later, and centrifuged at 20,000 g for 10 min at 4°C to remove cell debris. To enrich secreted proteins in the conditioned media, conditioned media samples were centrifuged using Amicon centrifugal filters with a 3kDa cutoff (Millipore, Billerica, MA). A total of 8 concentrated conditioned media samples were independently prepared: 4 samples from control siRNA-treated cells, and 4 samples from Galphas siRNA-treated cells. Samples were stored at –70°C until they were sent to the Mount Sinai Proteomics Core Facility.HPLC-isobaric tags for relative and absolute quantitation mass-spectrometry (iTRAQ MS) - Data analysis ProteinPilot 3.0 (AB Sciex) was used to search the MS/MS spectra for protein identification and quantitation with its searching algorithm Paragon 3.0.0.0 (*Reference). The protein database used for searching was Uniprot mouse fasta file (release-2010_11). The search parameters include quantitation for iTRAQ 8-plex (peptide-labeled), MMTS for cysteine alkylation, trypsin for enzyme digestion, biological modifications for ID focus, and taxonomy set for Mus musculus. The detected protein threshold was set to 1.3 (95% confidence). Additionally, we converted our AB Sciex mass spectral data (TOF/TOF data) into an mzML format, using the AB Sciex MS Data Converter (beta version 1.3) tool. Finally, we used the command line tool group2xml, which is included with ProteinPilot Software, to convert the .group search engine result file to an XML file.
Project description:The PXD project contains a project which aimed to identify protein evidences (missing proteins) from insoluble proteins from cell lysate by mass spectrometry. It involves the analysis of 3 human lung cell line and 3 liver cell lines,including the identification information and quantitative information.The raw data, peak data and search data were all cataloged into this project.