Quantitative analysis by next generation sequencing of hematopoietic stem and progenitor cells (LSK) and of splenic B cells transcriptomes from wild-type and Usp3-knockout mice

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• 作者：Cesare Lancini^a ; ¹ ; Gaetano Gargiulo^a ; ¹ ; Paul C.M. van den Berk^b ; Elisabetta Citterio^a ; ^{e.citterio@nki.nl" class="auth_mail" title="E-mail the corresponding author}
• 关键词：BM ; bone marrow ; DDR ; DNA damage response ; DUBs ; deubiquitinating enzymes ; HSC ; hematopoietic stem cell ; LSK ; Lin-Sca1+ cKit+ cells ; RNA-seq ; RNA sequencing ; Ub ; ubiquitin ; USP3 ; Ub-specific protease 3
• 刊名：Data in Brief
• 出版年：2016
• 出版时间：March 2016
• 年：2016
• 卷：6
• 期：Complete
• 页码：556-561
• 全文大小：1129 K

文摘

The data described here provide genome-wide expression profiles of murine primitive hematopoietic stem and progenitor cells (LSK) and of B cell populations, obtained by high throughput sequencing. Cells are derived from wild-type mice and from mice deficient for the ubiquitin-specific protease 3 (USP3; Usp3Δ/Δ). Modification of histone proteins by ubiquitin plays a crucial role in the cellular response to DNA damage (DDR) (Jackson and Durocher, 2013) an id="bbib1">[1]a>an>. USP3 is a histone H2A deubiquitinating enzyme (DUB) that regulates ubiquitin-dependent DDR in response to DNA double-strand breaks (Nicassio et al., 2007; Doil et al., 2008) [2]a> and [3]a>. Deletion of USP3 in mice increases the incidence of spontaneous tumors and affects hematopoiesis an id="bbib4">[4]a>an>. In particular, Usp3-knockout mice show progressive loss of B and T cells and decreased functional potential of hematopoietic stem cells (HSCs) during aging. USP3-deficient cells, including HSCs, display enhanced histone ubiquitination, accumulate spontaneous DNA damage and are hypersensitive to ionizing radiation (Lancini et al., 2014) an id="bbib4">[4]a>an>. To address whether USP3 loss leads to deregulation of specific molecular pathways relevant to HSC homeostasis and/or B cell development, we have employed the RNA-sequencing technology and investigated transcriptional differences between wild-type and Usp3Δ/Δ LSK, naïve B cells or in vitro activated B cells. The data relate to the research article “Tight regulation of ubiquitin-mediated DNA damage response by USP3 preserves the functional integrity of hematopoietic stem cells” (Lancini et al., 2014) an id="bbib4">[4]a>an>. The RNA-sequencing and analysis data sets have been deposited in NCBI׳s Gene Expression Omnibus (Edgar et al., 2002) an id="bbib5">[5]a>an> and are accessible through GEO Series accession number GSE58495 (an id="ir0005" class="interref" data-locatorType="url" data-locatorKey="http://www.ncbi.nlm.nih.gov.ezproxy.uned.es/geo/query/acc.cgi?acc=GSE58495">http://www.ncbi.nlm.nih.gov.ezproxy.uned.es/geo/query/acc.cgi?acc=GSE58495a>an>). With this article, we present validation of the RNA-seq data set through quantitative real-time PCR and comparative analysis.