Fig. 1

Fig. 1 Mass spectrometry-based quantitative proteomics reveals changes in ECM composition during zebrafish spinal cord regeneration.

a Timeline of axonal regrowth and functional recovery after SCI in larval zebrafish. Timepoints of tissue collection for mass spectrometry (MS) analysis are indicated. b Time course of axonal regrowth after spinal cord transection. Shown is the same animal at different timepoints after SCI. Dashed lines indicate the dissected trunk region for MS analysis. Images shown are maximum intensity projections of the spinal lesion site (lateral view; rostral is left). c–d Heatmaps of matrisome proteins exhibiting differential abundance between lesioned (1 dpl, c; 2 dpl, d) and unlesioned age-matched groups (n = 3 independent biological replicates for each experimental group). Each column represents one biological replicate and each row one protein. Permutation-based FDR calculation, two-tailed Student’s t-test. Asterisks indicate matrisome proteins that are common to both timepoints. e Expression of the indicated genes, coding for differentially regulated matrisome proteins, is upregulated in the lesion site, as determined by in situ hybridization (ISH; lateral view; rostral is left). n ≥ 9 animals for each gene. f Expression of indicated genes, coding for differentially regulated matrisome proteins, is detected in the spinal cord stump, its immediate vicinity, or the highly disorganized lesion core (arrowhead), as determined by fluorescence ISH on transversal tissue sections (dorsal is up). Asterisks indicate staining artifacts. n ≥ 5 animals for each gene. a–f Scale bars: 250 µm (b, top), 100 µm (e), 25 µm (b, bottom), 20 µm (f). dpl days post-lesion, FC fold change, FDR false discovery rate, var variant.