Analysis of mRNA expression by RNAseq. (A) Raw numbers of differentially expressed mRNAs for the CMP comparisons indicated are shown (FDR cutoff for significance is 0.001). (B) Fold enrichment of let-7 target gene frequency in the indicated pools of transcripts compared with the overall frequency of let-7 targets among all analyzed mRNAs is shown. *, P < 0.001; hypergeometric p-values compared with the expected frequency of let-7 targets based on the frequency of targets among all expressed mRNAs. (C) GSEA demonstrating significant positive enrichment of the FL CMP transcriptional program in iLIN28B CMPs. Transcripts enriched in iLIN28B adult BM CMPs compared with adult BM CMPs were compared with the set of transcripts significantly enriched in WT FL CMPs compared with WT adult BM CMPs. NES, normalized enrichment score; NOM p, nominal p-value. (D) Venn diagram analysis showing overlap of transcripts up-regulated in FL CMPs and iLIN28B CMPs compared with WT BM CMPs (left), as well as down-regulated transcripts for these comparisons (right). The p-value for overlap of up-regulated transcripts is <2.2 × 10−16 (expected number of 16.22); the p-value for overlap of down-regulated transcripts is <2.2 × 10−16 (expected number of 39.15). Analysis was performed with Fisher’s exact test. (E) Heat map demonstrating relative expression levels of the transcripts commonly up-regulated or down-regulated in iLIN28B CMPs and WT FL CMPs compared with WT BM CMPs. Pertinent transcripts are denoted.
