Figure 2—figure supplement 2.

(A,B) Volcano plots of differentially expressed genes from Nr2f2-positive and -negative (Nr2f2^pos and Nr2f2^neg) endothelial cells identified using RNA-seq reads quantified with (A) RefSeq or (B) Ensembl, version 95 (Ens95) transcript annotations. Genes with significant enrichment (padj <0.05) are shown as red or blue (log₂ fold change >1 or <-1, respectively). Grey dots are genes that fall below statistical cutoffs. (A, B) Green dots are selected known vein-specific genes. (C) Venn diagram of genes with a common NCBI ID in Ens95 and RefSeq identified as significantly Nr2f2^pos-enriched using either annotation. (D) Correlation of log₁₀ average expression levels (n = 3) from indicated annotation for Nr2f2^pos-enriched genes identified selectively as such by Ens95 or RefSeq only (left plot) or both annotations (right plot). Data are not normally distributed, Spearman correlation, r values are indicated. (E) Log₁₀ average expression (n = 3) for Nr2f2^pos-enriched genes as quantified by each indicated annotation. Separate plots shown for genes selectively identified as Nr2f2^pos-enriched using Ens95 or RefSeq. Data are not normally distributed, Wilcoxon matched-pairs signed-rank test, p values are indicated. (F) Plots of commonly annotated genes identified as Nr2f2^pos-enriched only by Ens95 with indicated values from Ens95 (left plot) or RefSeq (right plot). (G) Pie charts showing the proportion of reference genes identified as Nr2f2^pos-enriched by Ens95 and RefSeq with indicated relative 3' UTR length. (H) Correlation of log₁₀ average expression from Nr2f2^pos RNA-seq (n = 3) quantified with each annotation for matched reference genes with same 3' UTR length or longer Ens95 or RefSeq 3' UTR length. Data are not normally distributed, Spearman correlation, r values are indicated. (I) Log₁₀ average expression (n = 3) as quantified by Ens95 or RefSeq for Nr2f2^pos-enriched genes lacking an Ens95 3' UTR annotation. Data are not normally distributed, Wilcoxon matched-pairs signed-rank test, p value is indicated. (J) UCSC browser image of the erg gene (on minus strand) showing 3' UTR annotation and lack thereof from RefSeq and Ens95, respectively. Mapped depth of RNA-seq reads from Nr2f2^pos cells captured for each annotation is indicated. Genome-mapped consolidated reads from GSE32900 are also shown as is the location of 3P-seq feature, also on the minus strand.