Figure 4.

Analysis of DKO and Otx2KO Transcriptomes

(A–H) Venn diagrams showing the different categories of gene transcripts (boxes from (a) to (o) in each Venn diagram) up- or downregulated in DKO (A–D) and Otx2KO (E–H) ESCs in LIF + FBS when compared with WT ESCs (LIF + FBS) or WT ESCs (LIF + 2i) or WT EpiLCs (44 hr); this analysis allows us to identify DKO (LIF + FBS) gene transcripts shared with those up- or downregulated specifically in WT EpiLCs (44 hr) or WT ESCs (LIF + FBS) (red circle in box [j] in A–D); the same analysis was performed to identify Otx2KO ESCs (LIF + FBS) transcripts shared with those specifically expressed in WT ESCs (LIF + FBS) and WT ESCs (LIF + 2i) (red circle in box [j] in E–H).

(I–L) RT-PCR assays of selected genes up- or downregulated specifically in DKO (LIF + FBS) and WT EpiLCs (44 hr) (I), or in DKO (LIF + FBS) and WT ESCs (LIF + FBS) (J), or in Otx2KO (LIF + FBS) and WT ESCs (LIF + FBS) (K), or in Otx2KO (LIF + FBS) and WT ESCs (LIF + 2i) (L).

The selected genes belong to the box (j) highlighted with red circles in the Venn diagrams (n = 3 independent experiments).

See also Figure S5 and Table S3. Up- and Downregulated Gene Transcripts Detected in All Comparisons, Related to Figures 4 and S5, Table S4. List of Up- and Downregulated Transcripts as They Appear within Each Box of the Venn Diagrams Shown in Figures 4 and S5M-P, Related to Figures 4 and S5M–S5P, Table S5. List of Up and Downregulated Gene Transcripts Reported in Box (j) of Each Venn Diagram Shown in Figures 4 and S5M-P, Related to Figures 4 and S5M–S5P.