RNA from HSCs (LSK CD150+CD48) and CLPs (LIN SCA-1loC-KITloCD127+) from control and Zeb1–/– mice 14 days after the last dose of pIpC injection was extracted using the RNAeasy Micro Kit (QIAGEN). Total RNA quality and quantity were assessed using Agilent 2100 Bioanalyzer and the RNA Nano 6000 Kit (Agilent Technologies). The library was prepared using the NEB Ultra II Directional RNA Library Prep Kit for Illumina. The libraries then were sequenced using a 75 base paired end (2 × 75bp PE) dual index read format on the Illumina HiSeq4000 according to the manufacturer’s instructions. Further details on sequencing and bioinformatics were described previously (66).

The heatmap was created using Morpheus, an online tool, (Broad Institute). DEGs with an FDR of less than 0.05 were used for heatmaps. The biological pathway analysis was performed using BioCarta, KEGG, and Reactome pathway databases run on GSEA software (94) as well as IPA software (QIAGEN). IPA was used to create a prediction network of Zeb1 interactions with its target genes.

RNA-Seq for EPCAM+ and EPCAM from Zeb1–/– mice is described in Supplemental Methods.

All RNA-Seq data are available in the NCBI’s GEO database (GSE153664, GSE154615).

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