Extended Data Fig. 6: Technical properties of the LCM-seq dataset.
a, Boxplots comparing the number of genes observed per sample in different protocols. All samples were down-sampled to 1 million reads for comparison. For the dataset presented in main Fig. 3, the protocol relying on random priming was used. N represent numbers of samples or cells as indicated on the graph. Boxplot elements are defined in the Methods section (section on data visualization). Smart-Seq2 data is from ref. 21, bulk transcriptome data is from ref. 7. b, Representative images of samples collected for LCM-seq; scale bar: 100µm. c, Immunofluorescence staining of a BM arteriole stained for Col1a1, Pdpn and CD31. Scale bar: 20 µm. The experiment was repeated independently 4 times with similar results. d, Schwann cell markers were lowly expressed across all niches e, haematopoietic markers were highly expressed across all niches. In panel d and e, sample sizes are as follows: Arteriolar niches, n=28, endosteal niches, n=12, sinusoidal niches, n=14, non-vascular niches, n=11, sub-endosteal niche, n=11. Boxplot elements are defined in the Methods section (section on data visualization).
