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SGCs are difficult to investigate due to their flattened shape and tight physical connection to neurons\n                    <ns4:italic>in vivo<\/ns4:italic>\n                    and their rapid changes in phenotype and protein expression when cultured\n                    <ns4:italic>in vitro<\/ns4:italic>\n                    . Consequently, several aspects of SGC function under normal conditions as well as after a nerve injury remain to be explored. The recent advance in single cell RNA sequencing (scRNAseq) technologies has enabled a new approach to investigate SGCs.\n                  <\/ns4:p>\n                  <ns4:p>\n                    <ns4:bold>Methods:<\/ns4:bold>\n                    In this study we used scRNAseq to investigate SGCs from mice subjected to sciatic nerve injury. We used a meta-analysis approach to compare the injury response with that found in other published datasets. \u00a0Furthermore, we also used scRNAseq to investigate how cells from the dorsal root ganglion (DRG) change after 3 days in culture.\n                  <\/ns4:p>\n                  <ns4:p>\n                    <ns4:bold>Results:<\/ns4:bold>\n                    From our meta-analysis of the injured conditions, we find that SGCs share a common signature of 18 regulated genes following sciatic nerve crush or sciatic nerve ligation, involving transcriptional regulation of cholesterol biosynthesis. We also observed a considerable transcriptional change when culturing SGCs, suggesting that some differentiate into a specialised\n                    <ns4:italic>in vitro<\/ns4:italic>\n                    state while others start resembling Schwann cell-like precursors.\n                  <\/ns4:p>\n                  <ns4:p>\n                    <ns4:bold>Conclusion:<\/ns4:bold>\n                    By using integrated analyses of new and previously published scRNAseq datasets, this study provides a consensus view of which genes are most robustly changed in SGCs after injury. Our results are available via the Broad Institute Single Cell Portal, so that readers can explore and search for genes of interest.\n                  <\/ns4:p>","DOI":"10.12688\/wellcomeopenres.17885.1","type":"journal-article","created":{"date-parts":[[2022,5,19]],"date-time":"2022-05-19T09:15:18Z","timestamp":1652951718000},"page":"156","update-policy":"https:\/\/doi.org\/10.12688\/wellcomeopenres.crossmark-policy","source":"Crossref","is-referenced-by-count":31,"title":["Comparative transcriptional analysis of satellite glial cell injury response"],"prefix":"10.12688","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2480-0024","authenticated-orcid":false,"given":"Sara Elgaard","family":"Jager","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5869-8929","authenticated-orcid":false,"given":"Lone 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Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-156\/v1\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-156\/v1\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-156\/v1\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,3]],"date-time":"2023-10-03T03:35:15Z","timestamp":1696304115000},"score":1,"resource":{"primary":{"URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-156\/v1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,5,19]]},"references-count":65,"URL":"https:\/\/doi.org\/10.12688\/wellcomeopenres.17885.1","relation":{"has-review":[{"id-type":"doi","id":"10.21956\/wellcomeopenres.19811.r50906","asserted-by":"subject"},{"id-type":"doi","id":"10.21956\/wellcomeopenres.19811.r50916","asserted-by":"subject"},{"id-type":"doi","id":"10.21956\/wellcomeopenres.19811.r50916","asserted-by":"object"},{"id-type":"doi","id":"10.21956\/wellcomeopenres.19811.r50906","asserted-by":"object"}],"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.11.22.469443","asserted-by":"object"}]},"ISSN":["2398-502X"],"issn-type":[{"value":"2398-502X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,5,19]]},"assertion":[{"value":"Indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-156\/v1#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.21956\/wellcomeopenres.19811.r50906, Temugin Berta, Pain Research Center, Department of Anesthesiology, University of Cincinnati Medical Center, Cincinnati, OH, 24 Jun 2022, version 1, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-156\/v1#referee-response-50906","order":0,"name":"referee-response-50906","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Sara Jager<\/b>; \n<i>Posted: 14 Oct 2022<\/i>; Thank you very much for reviewing our work and adding your perspective on the study.","URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-156\/v1#referee-comment-5147","order":1,"name":"referee-comment-5147","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/wellcomeopenres.19811.r50916, Kyle M. Baumbauer, Department of Cell Biology and Physiology,, University of Kansas Medical Center, Kansas City, KS, 27 Jul 2022, version 1, indexed","URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-156\/v1#referee-response-50916","order":2,"name":"referee-response-50916","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Sara Jager<\/b>; \n<i>Posted: 14 Oct 2022<\/i>; Thank you very much for reviewing our work and your views on the field.  We do detect a common injury signature in the SNI and nerve crush SGCs, it just does not include many genes (Fig 2E-F). As you write, other genes might also belong to this common signature, but our power to detect differentially regulated genes are tempered by the limitations associated with single cell RNAseq (e.g. shallow sequencing).  We agree with your suggestions for why we do not detect \n<i>Gfap<\/i> or \n<i>Gja1<\/i> regulation. It could indeed be due to restricted time points or only regulation in a subset of SGCs. We think it unlikely to be due to Schwann cell reversion, since it has previously only been observed after substantial time in culture, and our cells were processed within a few hours of dissection.  We also agree that gene expression is affected by enzymatic dissociation. This is well established in the literature (e.g. https:\/\/www.hubrecht.eu\/app\/uploads\/2017\/11\/VanOudenaarden_Key_2017-VanDenBrink_Single-cell-sequencing-reveals-dissociation-induced-gene-expression-in-tissue-subpopulations.pdf). However, beyond the expected immediate early gene induction, it remains a known unknown which transcripts would have been affected in our dataset, until additional in situ experiments have been conducted.  The clustering performed in our paper is based on the 2000 genes that vary most between cell types. It does not rely on traditional SGC markers. Our analysis of cholesterol biosynthesis genes therefore only reveals that their expression is regulated after nerve injury, not whether these genes will be good markers for SGCs.","URL":"https:\/\/wellcomeopenresearch.org\/articles\/7-156\/v1#referee-comment-5148","order":3,"name":"referee-comment-5148","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"This work was supported by the Lundbeck foundation (R313-2019-606, R286-2018-2016 and R293-2018-960), The Wellcome trust (218452) and The Independent Research fund Denmark (8048-00072A). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":4,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}