Supplementary Figure 5: Sample clustering tree is not affected by the inclusion of other tissue samples or changes in gene-selection criteria.

(a) Sample clustering tree based on expression of differentially expressed genes (protein coding and lncRNA genes differentially expressed in at least one pairwise comparison between the 10 cell types in the dataset [each with 2 replicates, fold change >2, false discovery rate<5%]). The tree was obtained from randomly sub-sampled data to control for differences in sequencing depth. Publicly available RNA-Seq data (Supplementary Table 3) included: the human body map project (adrenal, lymph node, lung, colon, prostate, ovary, adipose, breast, kidney, thyroid, heart, testis, brain, liver, muscle, peripheral blood leucocytes, and a mix of these tissues), primary CD19+ B cells, CD3+ T cells, CD4+ T cells, and CD8+ T cells, four replicates of mobilized peripheral blood CD34+ cells (MPB CD34+ (1), (2), (3) and (4)), and bone marrow CD34+ cells (BM CD34+) (all labeled in grey). (b) Sample clustering trees based on expression of genes that are differentially expressed in at least one pairwise comparison between the 10 cell types, using a range of fold change and false discovery rate (FDR) criteria for selection of differentially expressed genes. Number of differentially expressed genes (N) identified for each criteria combination is depicted above the corresponding tree. Two biological replicates for each of the 10 cell types are depicted. H: HSC; L: LMPP; C: CLP; B: BCP; T1: Thy1; T2: Thy2; T3: Thy3; T4: Thy4; T5: Thy5; T6: Thy6 (all labeled in color).