The code for the manuscript:

FOXK1 regulates Wnt signaling to promote cardiogenesis

Javier E. Sierra-Pagan, Nikita Dsouza, Satyabrata Das, Thijs A. Larson, Patricia Stan, Erik J. Wanberg, Mary G. Garry, Wuming Gong, Daniel J. Garry

Main Figures

Figure 2

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GO pathway analysis highlights pathways and development related terms in D3 control EBs, the x-axis represents the counts of genes in each GO term.	Fig. 2a	R
The heatmap represents upregulated and downregulated in the control EBs vs. the Foxk1 KO EBs at D3	Fig. 2b	R
GO pathway analysis highlights pathways and development related terms in D5 control EBs, the x-axis represents the counts of genes in each GO term.	Fig. 2c	R
The heatmap represents upregulated and downregulated in the control EBs vs. the Foxk1 KO EBs at D5	Fig. 2d	R

Figure 3

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Enriched heatmap of the nucleoATAC data showing more nucleosome free regions (NFR) in control samples as compared to Foxk1 KO samples at D3 at the Foxk1 binding sites.	Fig. 3a	R
Enriched heatmap of the nucleoATAC data showing more nucleosome free regions (NFR) in control samples as compared to Foxk1 KO samples at D5 at the Foxk1 binding sites.	Fig. 3b	R
Venn Diagram shows the overlap of increased accessibility and upregulated genes between ATACseq and RNAseq, respectively, in the control group at D3 over the Foxk1 KO group	Fig. 3c	R
Venn Diagram shows the overlap of increased accessibility and upregulated genes between ATACseq and RNAseq, respectively, in the control group at D5 over the Foxk1 KO group	Fig. 3d	R
The heatmap shows commonly expressed transcription factors in both the ATACseq and RNAseq datasets upregulated and downregulated in the control EBs over the Foxk1 KO EBs at D3.	Fig. 3e	R
The heatmap shows commonly expressed transcription factors in both the ATACseq and RNAseq datasets upregulated and downregulated in the control EBs over the Foxk1 KO EBs at D5.	Fig. 3f	R

Figure 4

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Pathway analysis highlights GO pathways and development related terms in D10 control EBs, the x-axis represents the counts of genes in each GO term.	Fig. 4e	R
The heatmap shows significantly (adjusted p-value < 0.05) differentially expressed transcripts upregulated and downregulated with a two fold between control EBs vs. Foxk1 null EBs at D10.	Fig. 4f	R
The heatmap represents a significant (adjusted p-value < 1e-04) change in chromatin accessibility at D10 for control and Foxk1 KO.	Fig. 4g	R

Figure 5

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RNAseq pathway analysis of Wnt signaling in D5 EBs comparing control and Foxk1 KO groups.	Fig. 5a	R
The PCA of RNAseq of EB differentiation at D10 shows samples with similar gene expression cluster together.	Fig. 5e	R
Venn diagram shows 320 genes up-regulated in both Ct and KO + IWR1 samples when compared to Foxk1 KO samples	Fig. 5f	R
Top 10 GO pathways and development terms significantly enriched using the genes commonly upregulated in control and Foxk1 KO + IWR1 conditions.	Fig. 5g	R
The heatmap shows top 20 genes from two GO terms (muscle tissue development and striated muscle tissue development) commonly upregulated in control and Foxk1 KO + IWR1 samples.	Fig. 5h	R

Figure 6

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Heatmap highlighting the top 20 transcription factors associated with the Wnt signaling pathway enriched in the Foxk1 null D5 EB group from the RNA-seq dataset	Fig. 6a	R
A region upstream of Wnt6 (chr1:74,770,049-74,773,057) that contains a FOXK1 DNA motif, β-catenin binding site and decreased chromatin accessibility in the absence of Foxk1 compared to control EBs at D5	Fig. 6c	link

Supplementary Figure 3

Supplementary Figure 3

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The heatmap shows pathways significantly enriched in either control or Foxk1 KO showing cardiac related pathways enriched in control D3.	Supplementary Fig. 3a	R
The heatmap shows pathways significantly enriched in either control or Foxk1 KO showing cardiac related pathways enriched in control D5.	Supplementary Fig. 3b	R
The word cloud shows genes up-regulated in control at D3 with the size directly representing a log2 transformed fold change (log2FC)	Supplementary Fig. 3c	R
The word cloud shows genes up-regulated in control at D5 with the size directly representing a log2 transformed fold change (log2FC)	Supplementary Fig. 3d	R
The barplot shows GO pathway analysis highlighting pathways and development terms enriched in The Foxk1 KO D3 respectively.	Supplementary Fig. 3e	R
The barplot shows GO pathway analysis highlighting pathways and development terms enriched in The Foxk1 KO D3 and D5 respectively.	Supplementary Fig. 3f	R

Supplementary Figure 4

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The word cloud are commonly upregulated transcription factors between D3.	Supplementary Fig. 4a	R
The word cloud are commonly upregulated transcription factors between D5.	Supplementary Fig. 4b	R
Top 5 significantly enriched GO terms using genes that overlap between ATACseq and RNAseq at D3	Supplementary Fig. 4c	R
Top 5 significantly enriched GO terms using genes that overlap between ATACseq and RNAseq at D5	Supplementary Fig. 4d	R

Supplementary Figure 5

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The top 15 enriched GO pathways, highlighting pathways and development related terms in the Foxk1 null at D10.	Supplementary Fig. 5a	R

GEO Accession numbers

The superseries accession number for the project: GSE202563

GEO Accession	Link
GSE202517	ATAC
GSE202562	RNA