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Fig. 1 | Genome Biology

Fig. 1

From: Single-cell transcriptomic reconstruction reveals cell cycle and multi-lineage differentiation defects in Bcl11a-deficient hematopoietic stem cells

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+4834135. 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

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