{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T09:46:18Z","timestamp":1753868778693,"version":"3.41.2"},"reference-count":49,"publisher":"Wiley","issue":"8","license":[{"start":{"date-parts":[[2023,8,28]],"date-time":"2023-08-28T00:00:00Z","timestamp":1693180800000},"content-version":"vor","delay-in-days":27,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Current Protocols"],"published-print":{"date-parts":[[2023,8]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Adult stem cells play a critical role in the maintenance and repair of the organs in which they reside. However, their function is highly dependent on the crosstalk with their niche environment that changes during development and in disease states. The niche provides signals to stem cells to activate, proliferate, self\u2010renew, or remain in quiescence. In skeletal muscle, the niche is perturbed in disease contexts such as aging, muscular dystrophies, and cachexia. Therefore, it is important to develop methods that permit the decoupling of niche\u2010mediated from cell\u2010intrinsic changes that occur in muscle stem cells (MuSCs) in development and disease contexts. With the purpose of determining the effect of the niche environment on the MuSC transcriptome, function, or health, we have coupled an allogeneic stem cell transplantation system, meaning the transplantation of MuSCs from a donor mouse into a recipient host mouse, with Switching Mechanism at 5\u2019 End of RNA Template (SMART\u2010Seq) to quantify the effects of the niche on the MuSC transcriptome <jats:italic>in vivo<\/jats:italic>. Briefly, MuSCs are isolated from a GFP reporter donor mouse (Pax7\u2010nGFP) and transplanted into the irradiated muscles of immunocompromised allogeneic hosts. The MuSCs are re\u2010isolated by fluorescence\u2010activated cell sorting (FACS) after three weeks of inhabiting the heterologous niche, defined as a niche that is different from their originating niche, and sequencing\u2010ready libraries are created. This method allows for the direct comparison of the transcriptome of stem cells before and after transplantation into a host of a different age, disease status, or genetic background. This method can be used to accurately quantify the direct effect of the niche environment on the stem cell gene expression profile and to decouple cell\u2010intrinsic versus niche\u2010mediated alterations in the stem cell transcriptome. \u00a9 2023 The Authors. Current Protocols published by Wiley Periodicals LLC.<\/jats:p><jats:p><jats:bold>Basic Protocol<\/jats:bold>: Allogeneic muscle stem cell transplantation<\/jats:p>","DOI":"10.1002\/cpz1.877","type":"journal-article","created":{"date-parts":[[2023,8,28]],"date-time":"2023-08-28T13:28:41Z","timestamp":1693229321000},"source":"Crossref","is-referenced-by-count":0,"title":["Transcriptional Profiling of Skeletal Muscle Stem Cells After <i>In Vivo<\/i> Engraftment into a Heterologous Niche Environment"],"prefix":"10.1002","volume":"3","author":[{"given":"Felicia","family":"Lazure","sequence":"first","affiliation":[{"name":"Department of Human Genetics McGill University  Montr\u00e9al Quebec Canada"},{"name":"Lady Davis Institute for Medical Research Jewish General Hospital  Montr\u00e9al Quebec Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Darren M.","family":"Blackburn","sequence":"additional","affiliation":[{"name":"Department of Human Genetics McGill University  Montr\u00e9al Quebec Canada"},{"name":"Lady Davis Institute for Medical Research Jewish General Hospital  Montr\u00e9al Quebec Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vahab D.","family":"Soleimani","sequence":"additional","affiliation":[{"name":"Department of Human Genetics McGill University  Montr\u00e9al Quebec Canada"},{"name":"Lady Davis Institute for Medical Research Jewish General Hospital  Montr\u00e9al Quebec Canada"},{"name":"Present address: Department of Biochemistry, Microbiology &amp; Immunology, Faculty of Medicine University of Ottawa  ON Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2023,8,28]]},"reference":[{"doi-asserted-by":"publisher","key":"e_1_2_7_2_1","DOI":"10.1186\/gb\u20102010\u201011\u201012\u2010r119"},{"doi-asserted-by":"publisher","key":"e_1_2_7_3_1","DOI":"10.1002\/stem.1158"},{"doi-asserted-by":"publisher","key":"e_1_2_7_4_1","DOI":"10.1097\/MOT.0b013e3282f19f20"},{"doi-asserted-by":"publisher","key":"e_1_2_7_5_1","DOI":"10.1111\/febs.12273"},{"doi-asserted-by":"publisher","key":"e_1_2_7_6_1","DOI":"10.4161\/cc.20437"},{"doi-asserted-by":"publisher","key":"e_1_2_7_7_1","DOI":"10.1016\/j.celrep.2020.02.067"},{"doi-asserted-by":"publisher","key":"e_1_2_7_8_1","DOI":"10.1038\/s41598\u2010020\u201068098\u20109"},{"doi-asserted-by":"publisher","key":"e_1_2_7_9_1","DOI":"10.1038\/s41467\u2010017\u201000522\u20107"},{"doi-asserted-by":"publisher","key":"e_1_2_7_10_1","DOI":"10.1152\/ajpcell.00354.2010"},{"doi-asserted-by":"publisher","key":"e_1_2_7_11_1","DOI":"10.1016\/j.stem.2018.10.006"},{"doi-asserted-by":"publisher","key":"e_1_2_7_12_1","DOI":"10.1038\/s41596\u2010019\u20100278\u20108"},{"doi-asserted-by":"publisher","key":"e_1_2_7_13_1","DOI":"10.1101\/gr.127373.111"},{"doi-asserted-by":"publisher","key":"e_1_2_7_14_1","DOI":"10.1007\/s004419900062"},{"doi-asserted-by":"publisher","key":"e_1_2_7_15_1","DOI":"10.2144\/000114133"},{"doi-asserted-by":"publisher","key":"e_1_2_7_16_1","DOI":"10.1038\/ncb2015"},{"doi-asserted-by":"publisher","key":"e_1_2_7_17_1","DOI":"10.1038\/ncomms8087"},{"doi-asserted-by":"publisher","key":"e_1_2_7_18_1","DOI":"10.1242\/dev.115386"},{"doi-asserted-by":"publisher","key":"e_1_2_7_19_1","DOI":"10.1016\/j.cell.2007.03.044"},{"doi-asserted-by":"publisher","key":"e_1_2_7_20_1","DOI":"10.1177\/2472630318776594"},{"doi-asserted-by":"publisher","key":"e_1_2_7_21_1","DOI":"10.1016\/j.stemcr.2017.10.027"},{"doi-asserted-by":"publisher","key":"e_1_2_7_22_1","DOI":"10.15252\/embr.201949499"},{"doi-asserted-by":"publisher","key":"e_1_2_7_23_1","DOI":"10.1038\/s41467\u2010023\u201036265\u2010x"},{"doi-asserted-by":"publisher","key":"e_1_2_7_24_1","DOI":"10.1002\/adfm.202002924"},{"doi-asserted-by":"publisher","key":"e_1_2_7_25_1","DOI":"10.1016\/j.stem.2018.08.019"},{"doi-asserted-by":"publisher","key":"e_1_2_7_26_1","DOI":"10.1016\/j.stem.2018.12.014"},{"doi-asserted-by":"publisher","key":"e_1_2_7_27_1","DOI":"10.1016\/j.celrep.2018.03.091"},{"doi-asserted-by":"publisher","key":"e_1_2_7_28_1","DOI":"10.7554\/eLife.57393"},{"doi-asserted-by":"publisher","key":"e_1_2_7_29_1","DOI":"10.1242\/dev.057463"},{"doi-asserted-by":"publisher","key":"e_1_2_7_30_1","DOI":"10.1083\/jcb.9.2.493"},{"doi-asserted-by":"publisher","key":"e_1_2_7_31_1","DOI":"10.1186\/s13395\u2010015\u20100036\u20108"},{"doi-asserted-by":"publisher","key":"e_1_2_7_32_1","DOI":"10.1016\/0022\u2010510x(93)90224\u2010m"},{"doi-asserted-by":"publisher","key":"e_1_2_7_33_1","DOI":"10.1016\/j.cobme.2020.05.006"},{"doi-asserted-by":"publisher","key":"e_1_2_7_34_1","DOI":"10.1007\/s10974\u2010019\u201009550\u2010w"},{"doi-asserted-by":"publisher","key":"e_1_2_7_35_1","DOI":"10.3389\/fcell.2019.00254"},{"doi-asserted-by":"publisher","key":"e_1_2_7_36_1","DOI":"10.1007\/978\u20101\u201061779\u2010343\u20101_3"},{"doi-asserted-by":"publisher","key":"e_1_2_7_37_1","DOI":"10.1186\/s13395\u2010015\u20100067\u20101"},{"doi-asserted-by":"publisher","key":"e_1_2_7_38_1","DOI":"10.1038\/nprot.2014.006"},{"doi-asserted-by":"publisher","key":"e_1_2_7_39_1","DOI":"10.1038\/nm.3655"},{"doi-asserted-by":"publisher","key":"e_1_2_7_40_1","DOI":"10.1038\/nbt.3576"},{"doi-asserted-by":"publisher","key":"e_1_2_7_41_1","DOI":"10.1038\/s41467\u2010020\u201020760\u20106"},{"doi-asserted-by":"publisher","key":"e_1_2_7_42_1","DOI":"10.1016\/j.devcel.2009.05.008"},{"doi-asserted-by":"publisher","key":"e_1_2_7_43_1","DOI":"10.3389\/fcell.2022.1056523"},{"doi-asserted-by":"publisher","key":"e_1_2_7_44_1","DOI":"10.1016\/j.celrep.2020.107964"},{"doi-asserted-by":"publisher","key":"e_1_2_7_45_1","DOI":"10.1002\/ar.1091880206"},{"doi-asserted-by":"publisher","key":"e_1_2_7_46_1","DOI":"10.1016\/j.immuni.2016.10.016"},{"doi-asserted-by":"publisher","key":"e_1_2_7_47_1","DOI":"10.1016\/j.stem.2019.01.002"},{"doi-asserted-by":"publisher","key":"e_1_2_7_48_1","DOI":"10.1038\/nrm3265"},{"doi-asserted-by":"publisher","key":"e_1_2_7_49_1","DOI":"10.1111\/j.1469\u20107793.2000.t01\u20102\u201000333.x"},{"doi-asserted-by":"publisher","key":"e_1_2_7_50_1","DOI":"10.1152\/physrev.00043.2011"}],"container-title":["Current Protocols"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/currentprotocols.onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/cpz1.877","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,1,27]],"date-time":"2024-01-27T14:04:36Z","timestamp":1706364276000},"score":1,"resource":{"primary":{"URL":"https:\/\/currentprotocols.onlinelibrary.wiley.com\/doi\/10.1002\/cpz1.877"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,8]]},"references-count":49,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2023,8]]}},"alternative-id":["10.1002\/cpz1.877"],"URL":"https:\/\/doi.org\/10.1002\/cpz1.877","archive":["Portico"],"relation":{},"ISSN":["2691-1299","2691-1299"],"issn-type":[{"type":"print","value":"2691-1299"},{"type":"electronic","value":"2691-1299"}],"subject":[],"published":{"date-parts":[[2023,8]]},"article-number":"e877"}}