Fig. 4: Cells in PRIMO transcriptionally correlate with the MEF/KOSR substate and early mesodermal differentiation.
From: Generation and trapping of a mesoderm biased state of human pluripotency
a Principal component analysis of MIXL1-GFP(+)/SSEA-3(+) (dark purple stars) and MIXL1-GFP(−)/SSEA-3(+) (light purple stars) cells grown in PRIMO compared to the fractions identified in MEF/KOSR conditions (circles) and standard E8 culture (grey squares). b t-Distributed Stochastic Neighbour Embedding (t-SNE) plots of the expression of 45 genes in individual cells measured by Fluidigm Biomark qPCR and analysed by Monocle2. Displays all fractions in the same dimensional space from MEF/KOSR conditions (presented in Fig. 1c) MIXL1-GFP(−)/SSEA-3(+) cells as red squares, MIXL1-GFP(+)/SSEA-3(+) cells as green circles, MIXL1-GFP(−)/SSEA-3(+) cells as blue triangles and PRIMO conditions MIXL1-GFP(+)/SSEA-3(+) cells as purple stars. c Flow cytometry dot plot of the emerging population for which was sorted at the indicated timepoints during a differentiation time-course. Differentiation was induced incubating cells with E8 containing CHIRON at 3 µM for 72 h. d Principal component analysis of MIXL1-GFP(+)/SSEA-3(+) (dark purple stars) and MIXL1-GFP(−)/SSEA-3(+) (light purple stars) cells grown in PRIMO compared to the differentiation time course (coloured squares). e Gene expression scatter plot of bulk RNAseq analysis of cells grown in E8 compared to PRIMO medium. Differentially expressed genes were identified by DESeq2 with a cut off p value of <0.05 (blue squares) and the SeqMonk intensity difference filter with a p value cut off <0.05 (red squares). Some key genes related to pluripotency are shown as green squares. f Gene ontology (GO) statistical enrichment analysis was performed by ToppGene64 and Revigo62 on the list of genes from the SeqMonk59 intensity difference filter. GO terms which were significantly enriched are shown, the Log10 p values for each GO term are displayed. GO terms related to early differentiation and gastrulation are significantly enriched. b, e Source data are provided as a Source Data file.
