Data from six samples were used: two healthy controls, AML027 pre- and post-transplant, and AML035 pre- and post-transplant. Each sample was downsampled to ∼10k confidently mapped reads per cell. Then the gene-cell barcode matrix from each sample was concatenated. PCA, tSNE and
k-means clustering were performed on the pooled matrix, following the same steps outlined in PCA and tSNE analysis of PBMCs. For
k-means clustering,
K=10 was used based on the bend in the sum of squared error scree plot.
Cluster-specific genes were identified following the steps outlined in ‘Identification of cluster-specific genes and marker-based classification'. Classification was assigned based on cluster-specific genes, and based on expression of some well-known markers of immune cell types. ‘Blasts and Immature Ery 1' refers to cluster 4, which expresses
CD34, a marker of hematopoietic progenitors39 (
link), and
Gata2, a marker for early erythroids40 (
link). ‘Immature Ery 2' refers to clusters 5 and 8, which show expression of
Gata1, a transcription factor essential for erythropoiesis41 (
link), but not
CD71, which are often found in more committed erythroid cells39 (
link). ‘Immature Ery 3' refers to cluster 1, which show expression of
CD71. ‘Mature Ery' refers to cluster 2.
HBA1, a marker of mature erythroid cells, is preferentially detected in cluster 2. Cluster 3 was assigned as ‘Immature Granulocytes' because of the expression of early granulocyte markers such as
AZU1 and
IL8 (ref. 42 (
link)), and the lack of expression of
CD16. Cluster 7 was assigned as ‘Monocytes' because of the expression of
CD14 and
FCN1, for example. ‘B' refers clusters 6 and 9 because of markers such as
CD19 and
CD79A. ‘T' refers to cluster 10, because of markers such as
CD3D and
CD8A.
Zheng G.X., Terry J.M., Belgrader P., Ryvkin P., Bent Z.W., Wilson R., Ziraldo S.B., Wheeler T.D., McDermott G.P., Zhu J., Gregory M.T., Shuga J., Montesclaros L., Underwood J.G., Masquelier D.A., Nishimura S.Y., Schnall-Levin M., Wyatt P.W., Hindson C.M., Bharadwaj R., Wong A., Ness K.D., Beppu L.W., Deeg H.J., McFarland C., Loeb K.R., Valente W.J., Ericson N.G., Stevens E.A., Radich J.P., Mikkelsen T.S., Hindson B.J, & Bielas J.H. (2017). Massively parallel digital transcriptional profiling of single cells. Nature Communications, 8, 14049.