Spatial-ID: a cell typing method for spatially resolved transcriptomics via transfer learning and spatial embedding.

Spatially resolved transcriptomics provides the opportunity to investigate the gene expression profiles and the spatial context of cells in naive state, but at low transcript detection sensitivity or with limited gene throughput. Comprehensive annotating of cell types in spatially resolved transcriptomics to understand biological processes at the single cell level remains challenging. Here we propose Spatial-ID, a supervision-based cell typing method, that combines the existing knowledge of reference single-cell RNA-seq data and the spatial information of spatially resolved transcriptomics data. We present a series of benchmarking analyses on publicly available spatially resolved transcriptomics datasets, that demonstrate the superiority of Spatial-ID compared with state-of-the-art methods. Besides, we apply Spatial-ID on a self-collected mouse brain hemisphere dataset measured by Stereo-seq, that shows the scalability of Spatial-ID to three-dimensional large field tissues with subcellular spatial resolution.

SOBA: sequence ontology bioinformatics analysis.

The advent of cheaper, faster sequencing technologies has pushed the task of sequence annotation from the exclusive domain of large-scale multi-national sequencing projects to that of research laboratories and small consortia. The bioinformatics burden placed on these laboratories, some with very little programming experience can be daunting. Fortunately, there exist software libraries and pipelines designed with these groups in mind, to ease the transition from an assembled genome to an annotated and accessible genome resource. We have developed the Sequence Ontology Bioinformatics Analysis (SOBA) tool to provide a simple statistical and graphical summary of an annotated genome. We envisage its use during annotation jamborees, genome comparison and for use by developers for rapid feedback during annotation software development and testing. SOBA also provides annotation consistency feedback to ensure correct use of terminology within annotations, and guides users to add new terms to the Sequence Ontology when required. SOBA is available at http://www.sequenceontology.org/cgi-bin/soba.cgi.

A new two-dimensional CdII coordination polymer constructed by pyrazine-2,3-dicarboxylate.

In the title compound, poly[mu(5)-pyrazine-2,3-dicarboxylato-cadmium(II)], [Cd(C(6)H(2)N(2)O(4))](n) or [Cd(pdc)](n), where pdc is the pyrazine-2,3-dicarboxylate anion, the Cd(II) atom is six-coordinated by five carboxylate O atoms and one N atom from five different pdc ligands in a distorted octahedral CdO(5)N coordination geometry. Two Cd(II) atoms are bridged by carboxylate groups of the pdc ligands to create a dimeric unit. The dimeric units are further connected by the pdc ligands to generate an interesting two-dimensional structure.