Overview of SOX3 ChIP-Seq data from mouse neural progenitor cells.

<p>(A) Genomic classification of SOX3 binding sites relative to nearest transcriptional start sites. (B) Validation of SOX3 ChIP by qPCR. Fold change is relative to both input DNA and IgG control values for the same genomic location. Error bars correspond to standard deviation of three independent sample replicates, P-values indicated as <0.05 (ns), >0.05 (*) and >0.001 (**). (C) Highest enriched DNA motifs identified by MEME-ChIP as i. a SOX motif and ii. a SOX-POU motif. (D) Enriched Gene Ontology terms associated with subsets of SOX3 ChIP peaks.</p

Identification of common SOXB1 regulatory regions.

<p>(A) Overlap of this SOX3 ChIP-seq dataset with previously published SOX2 and SOX3 datasets from similar NPCs (2). (B) SOX motif identified with MEME-ChIP present in (i) all 648 SOXB1 common peaks and (ii) 295 peaks. (C) Average phastCons scores for the 648 SOXB1 peaks, showing more than 80% of peaks are either moderately (32%) or highly (42%) conserved. (D) Genomic localisation of the common SOXB1 peaks. Enriched Gene Ontology terms for (E) all 648 SOXB1 peaks and (F) both intronic and intergenic peaks.</p

SOX3 binding sites at enhancer regions.

<p>The overlap of SOX3 peaks with P300 binding sites identified from 11.5 dpc mouse; forebrain (A), midbrain (B), and limb (C), showing a high degree of overlap in the developing brain and not within the limb. Average phastCons score of the common peaks between SOX3 and P300 forebrain (D) and midbrain (E) binding sites.</p

Differentially expressed genes from <i>Sox3</i> null NPCs with nearby SOX3 ChIP binding sites.

<p>Differentially expressed genes from <i>Sox3</i> null NPCs with nearby SOX3 ChIP binding sites.</p

Evolutionary conservation of SOX3 bound regions.

<p>(A) The average phastCons score of each SOX3 bound peak showing 20% of peaks are highly conserved across 30 placental mammals. (B) A highly conserved peak within the second intron of <i>Dbx1</i> giving the highest conservation score of 0.97 (compared to all peaks). (C) A peak within the second intron of the neural gene <i>Nestin</i>, with an average phastCons score of 0.51.</p

Communication simulation training in medical education

Communication simulation training in medical educatio

Validation of putative Sox3 targets <i>in vivo</i>.

<p>A: <i>Dbx1</i> gene expression within whole 9.5 dpc embryos. B: <i>Dbx1</i> gene expression within 10.5 dpc dissected heads. C: qRT-PCR analysis of mRNA levels of <i>Sox1</i>, <i>Sox2</i>, <i>Slit1</i> and <i>Fezf2</i> showing no significant difference. RQ: relative quantification normalised to β-actin.</p

SOX3 binding sites surrounding <i>Dbx1</i>.

<p>A: Schematic diagram of previously published SOX3 binding sites (not to scale). B: <i>In vitro</i> ChIP validation of the five surrounding SOX3 binding sites (n = 3). C: <i>In vivo</i> ChIP validation of SOX3 binding to intronic site 2 in 10.5 dpc dissected heads (n = 3). All ChIP enrichment is relative to input and normalised to IgG IP.</p

Validation of putative Sox3 targets.

<p>A: qRT-PCR validation of gene expression levels of down regulated genes, <i>Dbx1</i> and <i>Fezf2</i> (n = 3). B: qRT-PCR validation of gene expression levels of up regulated genes <i>Ddr2</i>, <i>Slit1</i>, <i>Cspg5, Efnb3</i> and <i>Fam174b</i> (n = 3). C: Percentage of significantly regulated genes with SOX3 binding sites, as closest gene. RQ: relative quantification normalised to β-actin.</p

Sox3 expression in neural progenitor differentiation.

<p>A: Time course of <i>Sox3</i> gene expression levels by qRT-PCR throughout N2B27 differentiation (normalised to day 4 <i>Sox3</i> expression, n = 3). B: IHC of SOX3 showing expression at days 2, 4 and 6 of neuronal differentiation. C: GFP expressing cells sorted by FACS within <i>Sox3</i> null N2B27 differentiated ES cells at days 2, 4 and 7. D: qRT-PCR of <i>Sox1, Sox2, Sox2 and Pax6</i> expression at day 4 of N2B27 differentiation (n≥4). RQ: relative quantification normalised to β-actin.</p