Fig. 1

Single-cell transcriptome profiling of mouse HSCs by microfluidic system. a Gating strategy for HSC purification. Bcl11a ^+/+ and Bcl11a ^−/− HSCs were isolated by sorting markers LSK CD150⁺48⁻ and sBcl11a ^+/+ HSCs by markers LSK CD150⁺48⁻34⁻135⁻. Lineage markers used for enrichment included B220, CD19, CD3, CD4, CD8, TCRγδ, TCRβ, NK1.1, CD11b, Gr-1, Ter119. FSC: Forward scatter, SSC: Side scatter. b Single-cell capturing efficiency by the C1 AutoPrep microfluidic system and representative microscopic images of individual capture sites. A representative high-quality single HSC at an individual capture site is indicated by the red arrow. Representative pictures of poor quality cells, an empty capture site and a multiplet capture site are framed in colors as indicated in the key. c Principal component analysis of the transcriptome of all 181 HSCs passed initial computational quality control. One significant outlier from the Bcl11a ^+/+ dataset was identified (marked by red arrow). It was removed from subsequent analysis. d Boxplot comparing the number of genes detected (normalized count >1) in the sBcl11a ^+/+ and Bcl11a ^+/+ datasets. The two datasets were comparable, despite low sequencing depth of the sBcl11a ^+/+ dataset