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Additional file 2: Figure S2. Statistical analysis of serotonergic neurons number and cilia length in 72 hpf S. purpuratus SoxB2 knock-down experiments. a Embryonic nervous system (Synaptotagmin B by 1e11 immunohistochemistry) of uninjected control, MO-1, MO-2 and MO-Fluo embryos. The fluorescence of 1e11 positive neurons is shown in %, normalized by control uninjected embryos (100%). The intensity of staining from 10 embryos of each group was measured using ImageJ in three independent experiments. b Number of serotonergic neurons observed in six independent experiments using uninjected control, MO-1, MO-2 and MO-Fluo embryos. Serotonergic positive neurons were measured from at least 33 embryos in each experimental group. c Cilia length in uninjected control, MO-1, MO-2 and MO-Fluo embryos measured using the Zeiss confocal laser scanning LSM 510 microscope software. 10–12 cilia from at least 33 embryos were used in three independent experiments. Statistical analysis was performed using Prism 5 GraphPad software: P value versus uninjected controls = *P < 0.05, **P < 0.01, ***P < 0.001, while P value versus MO-Fluo = +P<0.05, ++P < 0.01, +++P < 0.001

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Additional file 4: Figure S3. Analysis of the cilia length in MO-injected embryos performed at 72 hpf pluteus. AcTubulin staining is shown in green and DAPI in blue. a control non injected embryo, b MO-1 injected embryo, c MO-2 injected embryo, d MO-Fluo injected embryo. Measurements of longest cilia length (l) are indicated in white. All cilia length measurements were performed using Ziess LSM Image Browser software. 10–12 cilia from at least 33 embryos in every experimental group were measured; scale bar is 20 µm

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Additional file 1: Figure S1. Control MO-Fluo in 72 hpf S. purpuratus embryos. Sea urchin embryos at 72 hpf from oral (a, b, c), lateral (a′, b′, c′) and vegetal (a″, b″, c″) views depict the tissues where fluorescence deriving from the fluorescent MO is visible (c–c″). Morphant embryos imaged with microscope (b–b″) present a phenotype similar to uninjected control embryos (a–a″)

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Additional file 3: Figure S4. Injection of MO-Fluo did not affect the development of Synaptotagmin B expressing neurons

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Additional file 5: Table S1. List of oligonucleotides used for qPCR experiments