Additional Supporting Information may be found in the online version of this article.

sc-12-1051_sm_SupplFigure1.tif1438KFigure S1. Ldb1 ChIP-seq of Lineage negative HSPCs. Sequence data from Ldb1 ChIP-seq study (55) was loaded onto the UC Santa Cruz genome browser as a custom track. Genes are shown that are also upregulated in LTO cells from the current study. The black boxes show the raw tags of sequences from the Ldb1 chromatin immunoprecipitation. The red arrows show genomic regions with high sequence tags denoting occupancy by Ldb1 protein. The RefSeq mRNA for each gene in shown in blue at the bottom of each browser snapshot.
sc-12-1051_sm_SupplFigure2.tif748KFigure S2. RNA-seq data on cell cycle regulators. WT and TG cells were co-cultured with OP9-DL1 stroma. WT progenitor cells did not survive past passage 5 but TG cells became immortalized. We performed RNA-seq on the WT and LTO RNA. Bar graphs show the FPKM values for each mRNA. Statistical comparisons were made using the DESeq program. The absence of an asterisk denotes no statistical significance between values. An asterisk shows statistical significance (with correction) and downward pointing arrows show which sample was compared. For example, for Ccnd1, DN cells were compared pairwise to all other samples and those with asterisks were significantly different (P<.05). The P values showed in red were generated by comparing grouped LTO samples versus grouped WT samples.
sc-12-1051_sm_SupplFigure3.tif641KFigure S3. RNA-seq data on cytokines and their receptors. Same description as above. P values shown in red are derived from group comparisons, LTO v. WT. Arrows denote specific pairwise comparisons but not grouped comparisons (e.g. Csf1r).
sc-12-1051_sm_SupplFigure4.tif475KFigure S4. RNA-seq data on apoptosis regulators. Same description as above. P values shown in red are derived from group comparisons, LTO v. WT.
sc-12-1051_sm_SupplFigure5.tif596KFigure S5. MIG and MIG-Cre transductions into Ldb1lox/lox T-cell progenitor cells as a control. Same experimental setup as in Figure 7. Ldb1lox/lox DN cells were sorted and transduced with MIG or MIG-Cre and plated on OP9-DL1 stroma. After 1-2 weeks of co-culture, the progenitor cells were analyzed for GFP (top panel); the GFP+ cells were gated and CD4/CD8 expression analyzed (bottom panel). The GFP expression was steadily lost during culture. Few progenitors were blocked at DN stage and MIGCre did not change this effect.
sc-12-1051_sm_SupplMethods.pdf107KSupplementary Data

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