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. 2021 Nov 3;16(11):e0252848. doi: 10.1371/journal.pone.0252848

Fig 7. FOXD3-AS1 expression and knockdown in hESCs.

Fig 7

(A) Log2 fold change between expression in hESCs and endoderm for all hit lncRNA transcripts in the screen whose loci were predicted to have RNA-based mechanisms of action (Fig 6). * = significant differential expression, sleuth q-value < 0.05. The LAMTOR5-AS1 hit TSS targeted in our screen could not resolve between 6 different LAMTOR5-AS1 transcripts (GENCODE transcript numbers in parantheses), and as such they are all plotted here. (B) RT-qPCR expression time course during definitive endoderm differentiation of H1 hESCs. (C) RT-qPCR expression of FOXD3-AS1 21 days post infection of H1 hESCs with FOXD3-AS1 shRNAs. *** = p < 0.001 by an unpaired t-test. (D) Phase-contrast images of H1 hESCs infected with FOXD3-AS1 shRNAs. Images were taken 21 days post infection. (E) RT-qPCR expression of pluripotency/differentiation genes 21 days post infection of H1 hESCs with FOXD3-AS1 shRNAs. * = p < 0.05, ** = p < 0.01, *** = p < 0.001 by an unpaired t-test. (F-H) FACS staining of day 5 definitive endoderm cells (F), day 5 early mesoderm cells (G), or day 12 neural progenitor cells (H) infected with scrambled shRNA or FOXD3-AS1 shRNA #1. Cells were fixed and stained with antibodies against FOXA2 and SOX17 (F), VIM and CD49e (G), or NES and PAX6 (H).