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      Spared Nerve Injury Causes Sexually Dimorphic Mechanical Allodynia and Differential Gene Expression in Spinal Cords and Dorsal Root Ganglia in Rats

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          Abstract

          Neuropathic pain is more prevalent in women. However, females are under-represented in animal experiments, and the mechanisms of sex differences remain inadequately understood. We used the spared nerve injury (SNI) model in rats to characterize sex differences in pain behaviour, unbiased RNA-Seq and proteomics to study the mechanisms. Male and female rats were subjected to SNI- and sham-surgery. Mechanical and cold allodynia were assessed. Ipsilateral lumbar dorsal root ganglia (DRG) and spinal cord (SC) segments were collected for RNA-seq analysis with DESeq2 on Day 7. Cerebrospinal fluid (CSF) samples for proteomic analysis and DRGs and SCs for analysis of IB-4 and CGRP, and IBA1 and GFAP, respectively, were collected on Day 21. Females developed stronger mechanical allodynia. There were no differences between the sexes in CGRP and IB-4 in the DRG or glial cell markers in the SC. No CSF protein showed change following SNI. DRG and SC showed abundant changes in gene expression. Sexually dimorphic responses were found in genes related to T-cells ( cd28, ctla4, cd274, cd4, prf1), other immunological responses ( dpp4, c5a, cxcr2 and il1b), neuronal transmission ( hrh3, thbs4, chrna4 and pdyn), plasticity ( atf3, c1qc and reg3b), and others ( bhlhe22, mcpt1l, trpv6). We observed significantly stronger mechanical allodynia in females and numerous sexually dimorphic changes in gene expression following SNI in rats. Several genes have previously been linked to NP, while some are novel. Our results suggest gene targets for further studies in the development of new, possibly sex-specific, therapies for NP.

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          The online version contains supplementary material available at 10.1007/s12035-021-02447-1.

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          Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

          In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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            Trimmomatic: a flexible trimmer for Illumina sequence data

            Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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              STAR: ultrafast universal RNA-seq aligner.

              Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases. To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy. STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/.
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                Author and article information

                Contributors
                fredrik.ahlstrom@helsinki.fi
                Journal
                Mol Neurobiol
                Mol Neurobiol
                Molecular Neurobiology
                Springer US (New York )
                0893-7648
                1559-1182
                30 July 2021
                30 July 2021
                2021
                : 58
                : 10
                : 5396-5419
                Affiliations
                [1 ]GRID grid.7737.4, ISNI 0000 0004 0410 2071, Department of Pharmacology, Faculty of Medicine, , University of Helsinki, ; Haartmaninkatu 8 (Biomedicum 1), 00014 Helsinki, Finland
                [2 ]GRID grid.7737.4, ISNI 0000 0004 0410 2071, Individualized Drug Therapy Research Program, Faculty of Medicine, , University of Helsinki, ; Haartmaninkatu 8 (Biomedicum 1), 00014 Helsinki, Finland
                [3 ]GRID grid.7737.4, ISNI 0000 0004 0410 2071, Laboratory of Molecular Neuroscience, Institute of Biotechnology, HiLIFE, , University of Helsinki, ; Viikinkaari 5D, 00014 Helsinki, Finland
                [4 ]GRID grid.7737.4, ISNI 0000 0004 0410 2071, Systems Biology/Pathology Research Group and Proteomics Unit, Institute of Biotechnology, HiLIFE, , University of Helsinki, ; 00014 Helsinki, Finland
                [5 ]GRID grid.15485.3d, ISNI 0000 0000 9950 5666, Department of Anaesthesiology, Intensive Care Medicine and Pain Medicine, , Helsinki University Hospital and University of Helsinki, ; Stenbäckinkatu 9, P.O. Box 440, 00029 Helsinki, Finland
                [6 ]GRID grid.5254.6, ISNI 0000 0001 0674 042X, Center for Translational Neuromedicine, Faculty of Health and Medical Sciences, , University of Copenhagen, ; Norre Allé 14, DK-2200 Copenhagen, Denmark
                [7 ]GRID grid.7737.4, ISNI 0000 0004 0410 2071, Department of Clinical Pharmacology, , University of Helsinki and Helsinki University Hospital, ; Tukholmankatu 8 C, 00014 Helsinki, Finland
                [8 ]GRID grid.7737.4, ISNI 0000 0004 0410 2071, SleepWell Research Programme, Faculty of Medicine, , University of Helsinki, ; Haartmaninkatu 3, 00014 Helsinki, Finland
                [9 ]GRID grid.15485.3d, ISNI 0000 0000 9950 5666, Emergency Medicine, , University of Helsinki and Department of Emergency Medicine and Services, Helsinki University Hospital, ; Haartmaninkatu 4, 00290 Helsinki, Finland
                Author information
                http://orcid.org/0000-0002-4120-8647
                Article
                2447
                10.1007/s12035-021-02447-1
                8497331
                34331199
                30a44abb-6581-48d7-ac59-5a108e8faac8
                © The Author(s) 2021

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 21 August 2020
                : 6 June 2021
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/100011102, Seventh Framework Programme;
                Award ID: FP7/2007–2013
                Funded by: FundRef http://dx.doi.org/10.13039/100010135, Finska Läkaresällskapet;
                Funded by: FundRef http://dx.doi.org/10.13039/100010665, H2020 Marie Skłodowska-Curie Actions;
                Award ID: 798944
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                © Springer Science+Business Media, LLC, part of Springer Nature 2021

                Neurosciences
                neuropathic pain,rat,sex-differences,behaviour,transcriptomics,proteomics
                Neurosciences
                neuropathic pain, rat, sex-differences, behaviour, transcriptomics, proteomics

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