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Fig. 5 | Genome Biology

Fig. 5

From: Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data

Fig. 5

In vivo qRT-PCR validation of candidate genes with altered 3 UTR length in proliferating cardiac fibroblasts. a Diagram showing different anatomical locations of an MI heart: remote zone (RZ) and infarct zone (IZ). b Representative immunofluorescence images showing EdU + cells in sham or indicated anatomical location of MI hearts. Scale bar indicates 50 µm. c qRT-PCR expression of proliferation marker genes in Pdgfra-GFP + cells sorted from sham hearts, and RZ and IZ samples. Shown is the mean expression and standard error (n=3), with stars indicating significant difference between comparisons (1-tail t test; p<0.05). d Sierra candidate genes exhibiting a shift to proximal or distal peak usage from scRNA-seq population F-Cyc in comparison to F-SH/F-SL. Shown is the difference in proximal to distal peak fold-change (log2). e qRT-PCR comparison of proximal to distal (P–D) peak expression from candidate genes in Pdgfra-GFP +cells (Additional file 2: Figure S7) sorted from sham hearts, and RZ and IZ samples. Y-axis represents ΔΔ (P–D) expression (log2; see the ‘Methods’ section) of sample comparisons RZ vs sham, IZ vs RZ, and IZ vs sham. Shown is the mean expression difference and standard error (n=3), with stars indicating a significant difference for the comparison (1-tail t test; p<0.05)

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