E-GEOD-48764 - RNA-seq transcriptome analysis of Nestin-GFP-peri and -GFP-retic bone marrow stromal cells

Released on 10 October 2013, last updated on 3 May 2014
Mus musculus
Samples (6)
Protocols (2)
Cell cycle quiescence is a critical feature contributing to haematopoietic stem cell (HSC) maintenance. Although various candidate stromal cells have been identified as potential HSC niches, the spatial localization of quiescent HSC in the bone marrow (BM) remains unclear. Here, using a novel approach that combines whole-mount confocal immunofluorescence imaging technique and computational modelling to analyse significant tridimensional associations among vascular structures, stromal cells and HSCs, we show that quiescent HSCs associate specifically with small arterioles that are preferentially found in endosteal BM. These arterioles are ensheathed exclusively by rare Nestin-GFP-peri/NG2+ pericytes, distinct from sinusoid-associated Nestin-GFP-retic/LepR+ cells. The present RNA-seq study sought to obtain a comprehensive understanding of the differences between the two distinct HSC cellular niches. mRNA profiles of sorted Nestin-GFP-peri and -GFP-retic bone marrow stromal cells were generated from pooled mice in triplicate by Illumina HiSeq 2000 sequencing.
Experiment type
RNA-seq of coding RNA 
Paul Frenette, Qiaozhi Wei
Arteriolar niches maintain haematopoietic stem cell quiescence. Kunisaki Y, Bruns I, Scheiermann C, Ahmed J, Pinho S, Zhang D, Mizoguchi T, Wei Q, Lucas D, Ito K, Mar JC, Bergman A, Frenette PS. , Europe PMC 24107994
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-GEOD-48764.idf.txt
Sample and data relationshipE-GEOD-48764.sdrf.txt
Additional data (1)E-GEOD-48764.additional.1.zip