Extensive transcriptome discovery based on the RNA-seq assay.

<p>(A) Our RNA-seq assay discovered over 8200 mRNAs that were not detected in microarray-based studies. (B) RNA quantities relative to those of the housekeeping gene beta-2 microglobulin (<i>B2m</i>) were correlated in qRT-PCR and RNA-seq assays, but variations were also observed in genes that were expressed at low levels. (C) Analysis of gene expression changes detected a transcriptionally active state in ST-HSCs with a larger number of genes than those considered previously. (D) We categorized genes into 4 classes; Class A and Class B, in which FC and FPKM , Class C (6332 genes), in which FC and FPKM , and Class D (6006 genes), in which FPKM . Class A and Class B represented DEGs, Class C represented steady-state transcription genes, and Class D represented genes with noisy expression and/or functional low-expression genes. (E) Enriched GO biological process (GO-BP) terms detected by DAVID (EASE score, , complete lists in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0093853#pone.0093853.s015" target="_blank">Tables S10</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0093853#pone.0093853.s016" target="_blank">S11</a>).