The Heisenberg-RIXS instrument at the European XFEL

Resonant Inelastic X-ray Scattering (RIXS) is an ideal X-ray spectroscopy method to push the combination of energy and time resolutions to the Fourier transform ultimate limit, because it is unaffected by the core-hole lifetime energy broadening. And in pump-probe experiments the interaction time is made very short by the same core-hole lifetime. RIXS is very photon hungry so it takes great advantage from high repetition rate pulsed X-ray sources like the European XFEL. The hRIXS instrument is designed for RIXS experiments in the soft X-ray range with energy resolution approaching the Fourier and the Heisenberg limits. It is based on a spherical grating with variable line spacing (VLS) and a position-sensitive 2D detector. Initially, two gratings are installed to adequately cover the whole photon energy range. With optimized spot size on the sample and small pixel detector the energy resolution can be better than 40 meV at any photon energy below 1000 eV. At the SCS instrument of the European XFEL the spectrometer can be easily positioned thanks to air-pads on a high-quality floor, allowing the scattering angle to be continuously adjusted over the 65-145 deg range. It can be coupled to two different sample interaction chamber, one for liquid jets and one for solids, each equipped at the state-of-the-art and compatible for optical laser pumping in collinear geometry. The measured performances, in terms of energy resolution and count rate on the detector, closely match design expectations. hRIXS is open to public users since the summer of 2022.Comment: 43 pages, 12 figures, Supplemental Materia

Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements

Zebrafish, a popular organism for studying embryonic development and for modeling human diseases, has so far lacked a systematic functional annotation program akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created a central repository to store and process zebrafish developmental functional genomic data. Our data coordination center ( https://danio-code.zfin.org ) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements throughout development, including classes with distinct features dependent on their activity in time and space. We delineated the distinct distance topology and chromatin features between regulatory elements active during zygotic genome activation and those active during organogenesis. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predicted functional relationships between them beyond sequence similarity, thus extending the utility of zebrafish developmental genomics to mammals