Transiting ultra-hot Jupiters are ideal candidates to study the exoplanet atmospheres and their dynamics, particularly by means of high-resolution, high signal-to-noise ratio spectra. One such object is KELT-20b, orbiting the fast rotating A2-type star KELT-20. Many atomic species have already been found in its atmosphere, with blueshifted signals that hints at the presence of a day-to-night side wind. We aimed to observe the atmospheric Rossiter-McLaughlin effect in the ultra-hot Jupiter KELT-20b, and to study any variation of the atmospheric signal during the transit. For this purpose, we analysed five nights of HARPS-N spectra covering five transits of KELT-20b. We computed the mean line profiles of the spectra with a least-squares deconvolution, and then we extracted the stellar radial velocities by fitting them with a rotational broadening profile in order to obtain the radial velocity time-series. We used the mean line profile residuals tomography to analyse the planetary atmospheric signal and its variations. We also used the cross-correlation method to study an already known double-peak feature in the FeI planetary signal. We observed both the classical and the atmospheric Rossiter-McLaughlin effect in the radial velocity time-series. The latter gave us an estimate of the radius of the planetary atmosphere that correlates with the stellar mask used in our work: R(p+atmo)/Rp = 1.13 +/- 0.02). We isolated the planetary atmospheric trace in the tomography, and we found radial velocity variations of the planetary atmospheric signal during transit with an overall blueshift of approximatively 10 km/s, along with small variations in the signals depth and, less significant, in the full width at half maximum (FWHM). We also find a possible variation in the structure and position of FeI signal in different transits.
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