Figure 4. Transcriptome analysis reveals close relationship between LSIG cells and ILC2.
(A) Flow cytometry analysis of the indicated cell surface markers (grey) by bone marrow LSIG cells. Open histograms depict staining with isotype-matched control antibodies.
(B,C) Quantitative RT-PCR analysis (± SEM; n=3) of expression of the indicated genes by LSIG cells (white bars) or ILC2 (black bars).
(D) Percentage (± SEM; n=4) of IL-5-producing bone marrow LSIG cells (white bars) compared to ILC2 from the small intestine (black bars).
(E) Hierarchical clustering of normalized microarray data of replicate RNA samples from the indicated cell subsets. Dendrogram was obtained by analyzing 911 out of 28,441 probesets.
(F) Heat map representation of genes clustering with at least two fold differences in expression pattern across different cell subsets as assessed by k-means. Columns represent the indicated cell subsets in 4 or 5 biological replicates. Each row represents one examined gene. Hierarchical clustering revealed 10 different clusters as indicated. The color code at the bottom defines the expression intensity of each individual gene in all examined cell subsets.
(G) Functional classification of the gene profiles shared by LSIG and ILC2 (i.e., ILC2/LSIG core cluster) and specific for ILC2 as assessed by k-means. Representative genes within these clusters are indicated. Signature gene expression profiles of the respective clusters used in the functional annotation are indicated above.
Data are representative of three independent experiments. ** p ≤ 0.01. LSIG: Lin− Sca1hiId2hiGATA3hi bone marrow cells. See also Figure S3.