Fig 2: Derivation of post-XEN cell lines from whole E6.5 embryos.(a) Gata6-mTomato × Cdx2-GFP embryo and post-XEN cell line X-E6.5-82278-4. From left to right: whole E6.5 embryo, large outgrowth of embryo after 5 days in culture, and established post-XEN cell line on day 60. The embryo and the outgrowth display intrinsic red fluorescence of mTomato, but the expression of mTomato in the post-XEN cell line is below the detection level of intrinsic red fluorescence from mTomato. (b) Immunofluorescence analysis of post-XEN cell line X-E6.5-82278-4. Expression of mTomato from the Gata6 promoter in the transgene is detectable with an antibody for RFP (first row, second column). Cells are immunoreactive (magenta) for XEN markers GATA4, GATA6, SOX7, SOX17, and DAB2. But cells are negative for ES cell markers OCT4 and NANOG, and for TS cell marker CDX2. Right-most column shows DAPI (blue).

Fig 3: The fold changes and correlation coefficients of four SOX7 potential target genes. (A–D) Four SOX7 target genes SPRY1, SLIT2, TRIB3 and MTHFD2, respectively, were selected based on the fold changes at the 3 time points in the SOX7-U219 dataset (upper panels) and the correlation coefficients in the BrCa759 dataset (lower panels; Log2 signal intensity). The coefficients and p values for the correlation are labeled.

Fig 4: Reporter assays to examine SOX7 effects on the transcription mediated by different promoters. (A) Predicted SOX7 consensus sites (pointed by ?) on the promoters of its potential target genes based on the Tfsitescan [29]. The first nucleotide of a transcription start site (TSS) is designated as “+1”, and the first nucleotide downstream TSS is “-1”. (B) Schematic diagram of a reporter construct with a 2 kb promoter driving the expression of Gluc. (C) Effects of ectopic SOX7 expression on the Gluc expression driven by the promoters of SPRY1, SLIT2, TRIB3 and MTHFD2, respectively. ** as p < 0.01, *** as p < 0.001.

Fig 5: A microarray study of MDA-MB-231 cells with DOX-inducible SOX7 expression. (A) A representative Western blot analysis of DOX-induced SOX7 expression in MDA-MB-231 cells. (B) In the microarray study, ectopically expressed SOX7 caused significant expression changes in genes of different functional groups. The p values are shown as “-log”. For example, the p values of the changes at the 3-time points of “Cell Death and Survival” genes are 5.0 × 10-10, 2.6 × 10-14, and 1.4 × 10-16, respectively. The overall p values increase from left to right. (C) The heat map of the microarray data showing the genes with altered expression between the samples with DOX-induced SOX7 and control. (D) Numbers of genes with at least 2-fold of activation or repression in MDA-MB-231 cells with DOX-inducible SOX7 collected at 6, 12 and 24 h after DOX addition.