Fig. 1

Tomo-Seq Identifies Genes with Spatially Restricted Expression in the Regenerating Heart

(A) Ventricular myl7:GFP expression is reduced at the wound border at 7 days post cryoinjury (dpi). In LUT (lookup table) images, GFP intensity below a threshold of 30% of signal intensity is displayed in red (GFP^low) while the rest is displayed in green (GFP^high). Boxed area is presented as magnified view,which shows examples of Mef2+, GFP^low cardiomyocytes expressing PCNA. Scale bars, 50 µm (overview) and 25 µm (magnified view).

(B) Average percentage of PCNA expressing GFP^low and GFP^high cardiomyocytes. Error bars represent SEM. Student’s t test, ***p = 0.0003.

(C) Cartoon summarizing the tomo-seq procedure. Cryoinjured zebrafish ventricles were sectioned from apex to base. RNA from single sections was extracted, followed by reverse transcription and barcoding, after which the samples were pooled for linear amplification and sequence library preparation.

(D) Pairwise correlation between individual sections across all genes detected at more than four reads in more than one section of the 3 dpi heart.

(E) Hierarchical clustering of Z score transformed expression profiles of all genes with expression peak (Z score > 1 in > 4 consecutive sections) in the 3 dpi heart. Zones I to III are marked by dashed yellow lines.

(F) Results of GO-term analysis using GOrilla for genes with spatially restricted expression in zones I, II, and III (based on gene lists in Data S2, S3, and S4) in the 3 dpi heart.