RNAseq for Nestin+ bone marrow stromal cells in normal and MLL-AF9 mice

Cumulative evidence points out to the importance of the bone microenvironment for leukaemic development. Our preliminary results show that bone marrow stem cells, identified by the expression of the intermediate filament protein nestin (Nestin+ cells), provide support and chemoresistance to leukaemic cells. The rationale for these experiments is that leukaemic/Nestin+ cells crosstalk might regulate Nestin+ cells genetic profile to become more supportive elements for leukaemia. Nestin expression level distinguish two different Nestin+ populations, which seem to possess distint characteristics. Therefore, we would like to separately study high-expressing (Nestin high) and low-expressing Nestin cells (Nestin low). From our in vitro results, Nestin+ cells seem to be providing detoxifying tools to leukaemic cells such as antioxidant aminoacids and enzymes. The aim of the project is to identify pathways and genes differentially regulated in Nestin+ high and/or low cells in a leukaemic background. The submitted samples have been taken by sorting Nestin+ high or low cells from normal or leukaemic mice. Some samples are from a single mouse whereas some others are pool of two mice (if number of cells was too little). The code for the samples is: N = normal mice L = leukaemic mice We have established four groups where we assume samples should be similar (just biological variability): (a) Nestin+ high cells from Normal mice (samples N1, N2, N3); (b) Nestin+ low cells from Normal mice (samples N4, N5, N6, N7, N8 and N9); (c) Nestin+ high cells from Leukaemic mice (samples L1, L2 and L3): (d) Nestin+ low cells from Leukaemic mice (samples L4, L5, L6 and L7)We would like to specially compare groups: (a)   versus (c); (b)  versus (d); (a)   versus (b); ((c)versus (d).