Wuming Gong, Satyabrata Das, Javier E. Sierra-Pagan, Erik Skie, Nikita Dsouza, Thijs A. Larson, Mary G. Garry, Edgar Luzete-Monteiro, Kenneth S. Zaret, Daniel J. Garry
Dataset | Format | Script | |
---|---|---|---|
ATAC-seq counts | link | SummarizedExperiment | R |
scRNA-seq of Etv2 induced reprogramming | link | SummarizedExperiment | R |
Bulk RNA-seq of EB differentiation induced by Etv2 Dox | link | SummarizedExperiment | |
A union set of Etv2 ChIP-seq peaks in ES/EB and MEFs | link | SummarizedExperiment | R |
Preprocessing Etv2 ChIP-seq, H3K27ac ChIP-seq and Brg1 ChIP-seq in ES/EB and MEF | link | R | |
Bash script for preprocessing the Brg1 KO H3K27ac ChIP-seq in MEF | bash | ||
Fastq datasets for ChIP-seq, ATAC-seq, bulkRNA-seq, scRNA-seq and NOMeseq | link |
Figures | Colab link | |
---|---|---|
The UMAP plot for the scRNA-seq of 948 undifferentiated MEFs, 3,539 reprogrammed cells at 24 hrs, 2,936 cells at 48 hrs and 7,202 cells at 7 days and 827 FLK1+/KDR cells at 7 days post-induction of ETV2 in MEFs | Fig. 1c | R |
The UMAP plot showing cell clusters from k-means clustering that identified seven distinct cell clusters | Fig. 1d | R |
The expression profiles of ETV2 and FLK1/KDR | Fig. 1e | R |
The volcano plot of genes differentially expressed between cluster 1 and cluster 7 | Fig. 1f | R |
The PCA of the variations of transcription factor (TF) associated chromatin accessibility of the ATAC-seq of MEF reprogramming (MEFs, 24 hrs, 48 hrs and 7 days post-induction) and EB differentiation (2.5 days and 3 hrs post induction) | Fig. 1h | R |
The 31 TF expression levels and motif associated chromatin accessibility consistently showed directional change in both EBs and MEFs (13 up-regulated TFs and 18 down-regulated TFs) | Fig. 1i | R |
Figures | Colab link | |
---|---|---|
The Venn diagram shows 131,001 and 18,024 Etv2 ChIP-seq peaks at 24 hrs post-induction during MEF reprogramming and 3 hrs post-induction in day 2.5 EBs, respectively | Fig. 2a | R |
The genomic distribution of EB specific, MEF specific and common ETV2 peaks. The EB and MEF specific ETV2 peaks were more likely distributed at the distal intergenic regions | Fig. 2b | R |
The heatmap shows the read density of MNase-seq, BRG1 ChIP-seq and H3K27ac ChIP-seq in MEFs, surrounding 131,001 ETV2 ChIP-seq peaks at 24 hrs post-induction during MEF reprogramming. The ETV2 peaks were divided into four quartiles based on the mean MNase-seq signals of the central 200-bp region | Fig. 2c | R |
The heatmap shows the ratio of NFR / nucleosome read density, read density of BRG1 ChIP-seq and H3K27ac ChIP-seq in EBs (day 2.5), surrounding 18,024 ETV2 ChIP-seq at 3 hrs post-induction. The ETV2 peaks were divided into NFR (5,291 peaks) and nucleosome (8,843 peaks) groups according to the local V-plot and fragment size profiles of ATAC-seq day 2.5 EBs without ETV2 induction | Fig. 2d | R |
The heatmap generated using NOMe-seq shows among 5,320 ETV2 binding sites that were nucleosome occupied at undifferentiated MEF, 4,744 (89.1%) became significantly nucleosome-free (NFR) while 576 (10.9%) stayed NOR at D1 of reprogramming | Fig. 2e | R |
Sequence motif analysis by DREME and CentriMo identified a common GGAAAT motif that were significantly more enriched in NFR regions compared with the nucleosomes in both MEFs and EBs | Fig. 2f | R |
A region upstream of Lmo2 that was highly enriched for nucleosomes in both cell types, as measured by MNase-seq and ATAC-seq was selected to perform in vitro nucleosomal binding assays | Fig. 2g | R |
Figures | Colab link | |
---|---|---|
The average partial Etv2 motif scores in upstream/downstream 500 bp regions surrounding the binding summit of the "early', "late" and "sustained" Etv2 peaks in EB differentiation and MEF reprogramming | Fig. 3a | R |
The percent of the "early', "late" and "sustained" Etv2 peaks in EBs and MEFs include partial Etv2 motifs in upstream/downstream 50bp regions surrounding the binding summits | Fig. 3b | R |
The heatmap shows the fold enrichment of ETV2 ChIP-seq, BRG1 ChIP-seq and H3K27ac ChIP-seq at 24 hrs, 48 hrs and 7 days post-induction of ETV2 | Fig. 3g | R |
The heatmap shows the fold enrichment of ETV2 ChIP-seq, BRG1 ChIP-seq and H3K27ac ChIP-seq, at 3 hrs and 12 hrs post-induction of ETV2 in day 2 EBs | Fig. 3h | R |
The Venn diagram shows the overlap between late ETV2 peaks in MEFs and EBs, as well as the overlap between the genes near the late ETV2 peaks | Fig. 3j | R |
Figures | Colab link | |
---|---|---|
VAE to 18,214 Etv2 ChIP-seq peaks during MEF reprogramming and identified six clusters of V-plot according to the central fragment size distribution | Fig. 4a | R |
The six clusters included three types of V-plots where the central Etv2 sites were nucleosome free (C1, C3 and C4), and three types of V-plots where the central Etv2 sites were nucleosome occupied (C2, C5, and C6), represented by aggregated V-plot | Fig. 4b | R |
The six clusters included three types of V-plots where the central Etv2 sites were nucleosome free (C1, C3 and C4), and three types of V-plots where the central Etv2 sites were nucleosome occupied (C2, C5, and C6), represented by NucleoATAC | Fig. 4c | R |
The six clusters included three types of V-plots where the central Etv2 sites were nucleosome free (C1, C3 and C4), and three types of V-plots where the central Etv2 sites were nucleosome occupied (C2, C5, and C6), represented by aggregated V-plot | Fig. 4d | R |
The six clusters included three types of V-plots where the central Etv2 sites were nucleosome free (C1, C3 and C4), and three types of V-plots where the central Etv2 sites were nucleosome occupied (C2, C5, and C6), represented by NucleoATAC | Fig. 4e | R |
The bar plot shows the proportion of each V-plot clusters in early, late and sustained Etv2 peaks, as well as in the background peaks | Fig. 4f | R |
The cluster labels of early, late and sustained ETV2 peak that were changed from MEF to D7 Flk1+ cells | Fig. 4g | R |
The fragment size distribution of ATAC-seq of FLK1+ cells vs. the mixture population at 12 hours post-ETV2 induction during EB reprogramming and day 7 post-ETV2 induction during MEF reprogramming. In both conditions, the mono-nucleosomes and the di-nucleosomes were significantly increased in the FLK1+ cell populations | Fig. 4h | R |
The aggregated V-plot whose centers are the ETV2 bound sites at FLK1+ cell populations at 12 hours post-ETV2 induction in EB, and at 7 days post-ETV2 induction | Fig. 4i | R |
Figures | Colab link | |
---|---|---|
The UMAP plot shows the scRNA-seq of 8,838 cells from day 7 post-induction in control MEFs, 1,502 FLK1+ cells from day 7 post-ETV2 induction in MEFs, 8,248 cells from day 7 post-ETV2 induction in Brg1 KD MEFs, and 8,034 cells at day 7 in Brg1 KD MEFs | Fig. 5c | R |
The UMAP plot shows the expression level of Etv2 | Fig. 5d | R |
The UMAP plot shows the expression level of Brg1 | Fig. 5e | R |
The UMAP plot shows the expression level of Flk1 | Fig. 5f | R |
Figures | Colab link | |
---|---|---|
The heatmap shows the piled up ATAC-seq signal surrounding the summit of 12,170 sustained ETV2 ChIP-seq peaks that were present at day 1 and day 7 post-induction of ETV2 in control MEFs (the sustained Etv2 peaks) | Fig. 6a | R |
The heatmap shows the transcription factors where motif associated chromatin accessibility were significantly changed at day 7 post-ETV2 induction in MEFs (unsorted MEFs or FLK1+ cells), or the Brg1 KD MEFs | Fig. 6b | R |
The genomic distribution of open ETV2 peaks and closed ETV2 peaks at 7 days post-ETV2 induction in Brg1 KD MEFs | Fig. 6c | R |
The aggregated V-plot of 1,204 ETV2 binding sites that were closed in MEFs and became open at day 1 post-ETV2 induction in MEFs | Fig. 6d | R |
Figures | Colab link | |
---|---|---|
The heatmap shows chromatin accessibility for transcription factors for control vs. Brg1 knockout during ES/EB differentiation | Fig. 7f | R |
The heatmap shows the ChIP-seq of sustained ETV2 binding sites in EB differentiation, and ATAC-seq of Control and Brg1 KO EBs at day 4 | Fig. 7g | R |
ATAC-seq V-plots of the genomic regions (640 bp) that are centered at ELK3 motifs | Fig. 7h | R |
Figures | Colab link | |
---|---|---|
The biological processes that are significantly associated with the up-regulated genes in cluster 7 (FLK1+ cells at day 7 of reprogramming) compared with cluster 1 (undifferentiated MEFs) | Extended Data Fig. 1h | R |
Figures | Colab link | |
---|---|---|
The violin plots show the scaled expression levels of endothelial markers such as Etv2, Emcn, Lmo2, Flk1/Kdr, Cdh5 and Sox18 in MEFs, day 1, day 2, day 7 post-ETV2 induction, as well as the FLK1+ cells from day 7 | Extended Data Fig. 2a | R |
The violin plots show the scaled expression levels of endothelial markers in seven cell clusters | Extended Data Fig. 2b | R |
The biological processes that are significantly associated with the up-regulated in genes in cluster 1 (undifferentiated MEFs) compared with the rest of the cell populations | Extended Data Fig. 2c | R |
GSEA plot indicates significant upregulation of the inflammatory response in MEFs (cluster 1) | Extended Data Fig. 2d | R |
Heatmap representing the gene expression levels scaled by Seurat for upregulated (red) and downregulated (blue) genes in cluster 1 and cluster 2 | Extended Data Fig. 2e | R |
The bar plots show top 10 significant pathways for cluster 1 MEFs | Extended Data Fig. 2f | R |
The bar plots show top 10 significant pathways for cluster 2 MEFs. | Extended Data Fig. 2g | R |
Figures | Colab link | |
---|---|---|
The UMAP shows expression profiles of Tlr3, Nfkb1 and Vav3, Cd38 and Abl1 (members of B cell receptor signaling pathway) in undifferentiated MEFs and post Etv2 induction day 1, day2, day 7 and Flk1+ cells at day 7 | Extended Data Fig. 3a | R |
The bar plot shows immune response related pathways significantly upregulated in Flk1+ cells from day 7 post Etv2 induction compared to MEFs | Extended Data Fig. 3b | R |
The bar plot shows immune response related pathways significantly upregulated in ay 1 post Etv2 induction compared to MEFs | Extended Data Fig. 3c | R |
Figures | Colab link | |
---|---|---|
The Venn diagrams show the overlap of commonly up-regulated genes during EB differentiation and MEF reprogramming | Extended Data Fig. 5a | R |
The Venn diagrams show the overlap of commonly down-regulated genes during EB differentiation and MEF reprogramming | Extended Data Fig. 5b | R |
Top commonly up-regulated genes during EB differentiation and MEF reprogramming | Extended Data Fig. 5c | R |
Top commonly down-regulated genes during EB differentiation and MEF reprogramming | Extended Data Fig. 5d | R |
The pathways that are significantly associated with commonly up-regulated genes during ES/EB differentiation and MEF reprogramming | Extended Data Fig. 5e | R |
The pathways that are significantly associated with commonly down-regulated genes during ES/EB differentiation and MEF reprogramming | Extended Data Fig. 5f | R |
Figures | Colab link | |
---|---|---|
The number of transcription factors whose motifs associated chromatin accessibility were significantly increased or decreased in the FLK1+ cell populations at 12 hours post-Etv2 induction compared with D2.5 EBs | Extended Data Fig. 6a | R |
The number of transcription factors whose motifs associated chromatin accessibility were significantly increased or decreased in the FLK1+ cell population at day 7 post-ETV2 induction compared with undifferentiated MEFs | Extended Data Fig. 6b | R |
The number of transcription factors whose motif associated chromatin accessibility that were commonly increased during EB and MEF reprogramming | Extended Data Fig. 6c | R |
The number of transcription factors whose motif associated chromatin accessibility that were commonly decreased during EB and MEF reprogramming | Extended Data Fig. 6d | R |
The transcription factors whose RNA-seq expression levels and motifs associated chromatin accessibility that were both up-regulated or down-regulated during EB reprogramming | Extended Data Fig. 6e | R |
The transcription factors whose RNA-seq expression levels and motifs associated chromatin accessibility that were both up-regulated or down-regulated during MEF reprogramming | Extended Data Fig. 6f | R |
The commonly up-regulated genes between EBs and MEFs | Extended Data Fig. 6g | R |
The commonly down-regulated genes between EBs and MEFs | Extended Data Fig. 6h | R |
The transcription factor motifs that are significantly enriched in 5k region surrounding the transcription start sites of the commonly up- and down-regulated genes in EBs and MEFs | Extended Data Fig. 6i | R |
Figures | Colab link | |
---|---|---|
The MNase-seq, BRG1, H3K27ac, H3, H3K9me3, H3K27me3, H3K9ac, H3K4me3, H4K7me1 and Hdac1 ChIP-seq signals surrounding the ETV2 bound sites at day1 post-ETV2 induction during MEF reprogramming, split into nucleosome and nucleosome free region (NFR) according to the MNase-seq signals | Extended Data Fig. 7a | R |
The latent representation of ATAC-seq V-plots (-320bp to + 320bp) where the centers are nucleosome free or occupied by mono nucleosome | Extended Data Fig. 7b | R |
The aggregated ETV2 bound sites centric V-plot whose centers were occupied by mono nucleosomes or nucleosome free | Extended Data Fig. 7c | R |
The fragment size profile of ETV2 bound sites centric region (-320bp to +320bp) where the centers are nucleosome free or occupied by mono nucleosomes | Extended Data Fig. 7d | R |
Motif analysis of ETV2 bound sites during EB reprogramming and MEF reprogramming | Extended Data Fig. 7e | R |
The overlap of ETV2 bound sites at day 1, day 2 and day 7 post-ETV2 induction during MEF reprogramming | Extended Data Fig. 7f | R |
The overlap of ETV2 bound sites at 3 hours and 12 hours post-ETV2 induction during EB reprogramming | Extended Data Fig. 7g | R |
The bar plot shows the percent of genes located near the late, early and sustained ETV2 bound sites related to blood vessel development | Extended Data Fig. 7h | R |
Figures | Colab link | |
---|---|---|
The expression profile of Dek expression during MEF reprogramming | Extended Data Fig. 9a | R |
The expression profile of Znhit1 expression during MEF reprogramming | Extended Data Fig. 9b | R |
The expression profile of Chd8 expression during MEF reprogramming | Extended Data Fig. 9c | R |
Figures | Colab link | |
---|---|---|
The heatmap shows the ATAC-seq signal surrounding the summit of 12,170 sustained ETV2 ChIP-seq peaks that were present at day 1 and day 7 post-induction of ETV2 in control MEFs | Extended Data Fig. 10a | R |
Heatmap shows ETV2 ChIP-seq signal surrounding 4,965 sustained ETV2 ChIP-seq peaks present in the D7 post ETV2 induction in WT MEFs and Brg1 KD MEFs | Extended Data Fig. 10b | R |
Figures | Colab link | |
---|---|---|
The plots show enrichment scores for each Histone Acetyltransferases' | Supplementary Fig. 1a | R |
The plots show enrichment scores for each Histone Deacetylases' | Supplementary Fig. 1b | R |
The plots show enrichment scores for each Inflammatory Response | Supplementary Fig. 1c | R |
The plots show enrichment scores for each NIK/NF-kappaB signaling | Supplementary Fig. 1d | R |
Figures | Colab link | |
---|---|---|
The plots show enrichment scores for each Histone Acetyltransferases' | Supplementary Fig. 2a | R R |
The plots show enrichment scores for each Histone Deacetylases' | Supplementary Fig. 2b | R R |
The plots show enrichment scores for each Inflammatory Response | Supplementary Fig. 2c | R R |
The plots show enrichment scores for each NIK/NF-kappaB signaling | Supplementary Fig. 2d | R R |
Figures | Colab link | |
---|---|---|
The plots show enrichment scores for each Histone Acetyltransferases' | Supplementary Fig. 3a | R |
The plots show enrichment scores for each Histone Deacetylases' | Supplementary Fig. 3b | R |
The plots show enrichment scores for each Inflammatory Response | Supplementary Fig. 3c | R |
The plots show enrichment scores for each NIK/NF-kappaB signaling | Supplementary Fig. 3d | R |
Figures | Colab link | |
---|---|---|
Venn diagram representing the overlap of common genes upregulated in ES/EB and MEF reprogramming post Etv2 induction, also overlapping with the genes from gene ontology terms for Histone Acetyltransferases' | Supplementary Fig. 4a | R |
Venn diagram representing the overlap of common genes upregulated in ES/EB and MEF reprogramming post Etv2 induction, also overlapping with the genes from gene ontology terms for Histone Deacetylases' | Supplementary Fig. 4b | R |
Venn diagram representing the overlap of common genes upregulated in ES/EB and MEF reprogramming post Etv2 induction, also overlapping with the genes from gene ontology terms for Inflammatory Response | Supplementary Fig. 4c | R |
Venn diagram representing the overlap of common genes upregulated in ES/EB and MEF reprogramming post Etv2 induction, also overlapping with the genes from gene ontology terms for NIK/NF-kappaB signaling | Supplementary Fig. 4d | R |
Figures | Colab link | |
---|---|---|
The transcription factors whose motif associated chromatin accessibility and expressions were up-regulated in both EB and MEF on Etv2 induction | Supplementary Fig. 5a | R |
The transcription factors whose motif associated chromatin accessibility and expressions were down-regulated in both EB and MEF on Etv2 induction | Supplementary Fig. 5b | R |
Figures | Colab link | |
---|---|---|
The PCA analysis of undifferentiated MEFs and Brg1 KD MEFs | Supplementary Fig. 6a | R |
The PCA analysis of different cell cycle programs | Supplementary Fig. 6b | R |
The bar plot showing cells in the G1 phase are increased with Brg1 KD in MEFs | Supplementary Fig. 6c | R |
The correction of cell cycle effects when combining the single cell RNA-seq data of undifferentiated MEFs and Brg1 KD MEFs | Supplementary Fig. 6d | R |
The correction of cell cycle effects when combining the single cell RNA-seq data of undifferentiated MEFs and Brg1 KD MEFs | Supplementary Fig. 6e | R |
The expression levels of Etv2 in cell-cycle effected adjusted single cell RNA-seq data from undifferentiated MEFs and Brg1 KD MEFs | Supplementary Fig. 6f | R |
The expression levels of Brg1 in cell-cycle effected adjusted single cell RNA-seq data from undifferentiated MEFs and Brg1 KD MEFs | Supplementary Fig. 6g | R |
The H3K27ac ChIP-seq signals of undifferentiated MEFs and Brg1 KD MEFs surrounding the early, late and sustained ETV2 bound sites in ETV2 induced MEF reprogramming | Supplementary Fig. 6h | R |
The datasets below belong to a SuperSeries GSE185684
Assay Type | GSE |
---|---|
ATACseq | GSE168636 |
ChIPseq | GSE168521 |
RNA-seq | GSE185682 |
scRNA-seq | GSE185683 |
NOMe-seq | GSE185681 |
The Mass Spectrometry data of ETV2 interacting proteins in D4 EBs.
https://github.com/gongx030/Etv2_pioneer/blob/master/massspec.xlsx
Figures | UCSC Genome browser | |
---|---|---|
Lmo2 locus | Figure 2g | Track |
All ChIP-seq data | Track | |
Rhoj promoter | Figure 14c | Track |
Kdr promoter | Figure 14c | Track |