Transcriptome analysis of Setdb1Mb1 pro-B cells reveals impaired pro-B to pre-B cell transition. Transcriptome analysis of Setdb1Mb1 pro-B cells reveals.

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Transcriptome analysis of Setdb1Mb1 pro-B cells reveals impaired pro-B to pre-B cell transition. Transcriptome analysis of Setdb1Mb1 pro-B cells reveals impaired pro-B to pre-B cell transition. (A) RNA-seq analysis performed on sorted control and Setdb1Mb1 pro-B cells (CD19+ IgD− IgM− Kit+ CD25−). Correlation plot shows expression levels of all genes in control and Setdb1-deficient pro-B cells as normalized RNA-seq read coverage in reads per kilobase per million reads (RPKM). Red dots, upregulated genes; blue dots, downregulated genes; black dots, genes with a less than 2-fold change in expression. (B) Deletion efficiency of the floxed Setdb1 allele in pro-B cells as determined by PCR on genomic DNA. In Setdb1Mb1 (Mb1-Cre; Setdb1flox/−) pro-B cells, absence of the flox band indicates complete deletion of the floxed exon 4. (C) GO term enrichment analysis of the dysregulated genes in Setdb1Mb1 pro-B cells was performed with GOStat (Beissbarth and Speed, 2004). P-values of the most highly enriched terms are plotted. (D) Gene set enrichment analysis of RNA-seq data from control and Setdb1Mb1 pro-B cells with gene lists representing Hardy Fr. A (B220+ CD43+ HSAlow BP-1−) and Fr. B/C (B220+ CD43+ HSAhigh). Setdb1Mb1 pro-B cells displayed a clear enrichment for the Fr. A signature, whereas Fr. B/C signatures were depleted. FDR, false discovery rate. Alessandra Pasquarella et al. Development 2016;143:1788-1799 © 2016. Published by The Company of Biologists Ltd