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

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 (US...

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Veröffentlicht in:Data in brief Jg. 6; S. 556 - 561
Hauptverfasser: Lancini, Cesare, Gargiulo, Gaetano, van den Berk, Paul C.M., Citterio, Elisabetta
Format: Journal Article
Sprache:Englisch
Veröffentlicht: Netherlands Elsevier Inc 01.03.2016
Elsevier
Schlagworte:
B cell
B-lymphocytes
Data
data collection
Deubiquitinating enzymes (DUBs)
DNA
DNA damage
DNA damage response (DDR)
DNA double-strand breaks (DSBs)
gene expression
hematopoiesis
Hematopoietic stem and progenitor cells (HSPC)
Hematopoietic stem cells (HSC)
Histone H2A
histones
homeostasis
LSK
mice
proteinases
quantitative analysis
quantitative polymerase chain reaction
RNA-seq
transcription (genetics)
Transcriptional profiling
transcriptome
Ubiquitin
Ubiquitin-specific protease 3 (USP3)
ubiquitination
Ubiquitin
DUBs
Deubiquitinating enzymes (DUBs)
Hematopoietic stem cells (HSC)
Histone H2A
LSK
USP3
DNA damage response (DDR)
BM
Ub
B cell
Hematopoietic stem and progenitor cells (HSPC)
DDR
Ubiquitin-specific protease 3 (USP3)
RNA-seq
HSC
Transcriptional profiling
DNA double-strand breaks (DSBs)
DUBs, deubiquitinating enzymes
LSK, Lin-Sca1+ cKit+ cells
BM, bone marrow
HSC, hematopoietic stem cell
Ub, ubiquitin
RNA-seq, RNA sequencing
USP3, Ub-specific protease 3
DDR, DNA damage response
ISSN:2352-3409, 2352-3409
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Zusammenfassung: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) [1]. 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) [2,3]. Deletion of USP3 in mice increases the incidence of spontaneous tumors and affects hematopoiesis [4]. 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) [4]. 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) [4]. The RNA-sequencing and analysis data sets have been deposited in NCBI׳s Gene Expression Omnibus (Edgar et al., 2002) [5] and are accessible through GEO Series accession number GSE58495 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE58495). With this article, we present validation of the RNA-seq data set through quantitative real-time PCR and comparative analysis.
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These authors contributed equally.
ISSN:2352-3409
2352-3409
DOI:10.1016/j.dib.2015.12.049