Technical Reports

Tang, Chen, Qian et al. present a multimodal, interpretable dimension reduction framework called SpaHDmap, which leverages histology images and enhances the resolution of spatial transcriptomics, thus enabling the dissection of complex tissue structures.

Yuan et al. present S2-omics, an end-to-end workflow that automatically identifies regions of interest in histology images to maximize molecular information capture in spatial omics experiments.

della Volpe et al. augment the ex vivo expansion potential of human haematopoietic stem cells (HSCs) by inhibiting ferroptosis with liproxstatin-1 or ferrostatin-1. Treated HSCs have enhanced in vivo repopulation capacity.

Zhou et al. design protein-based artificial kinetochore constructs as decoys to prevent premature chromosomal separation in aged oocytes. These constructs compete with chromosomal kinetochores, reducing excessive bipolar microtubule pulling forces.

Liu et al. present TemporalVAE, a method for integrating single-cell time course data. The model proposes a workflow to determine the biological timing of samples and its temporally sensitive genes, enabling single-cell developmental stage inference.

The authors identify a chemical cocktail to generate totipotent-like cells, which they then use to build an embryo model. This model captures a developmental spectrum from early embryogenesis to post-implantation events.

Wu, Zhang and colleagues introduce ‘compare and contrast spatial transcriptomics’ (CoCo-ST), a graph contrastive learning-based method for spatial transcriptomics analysis that detects low-variance structures.

Gao, Li and colleagues derive trophectoderm stem cells from 32-cell mouse embryos. These cells represent an early trophectoderm state and are capable of developing into placenta cells, forming placental organoids and contributing to blastoid generation.

Kefalopoulou, Rullens et al. develop Dam&ChIC to assay chromatin state at two different time points in the same cell. The method was used to study the reorganization of LADs during cell division and X chromosome inactivation.

Zhang, Hou, Ma et al. present PROFIT-seq, a sequencing strategy that involves adaptive sampling of transcriptome libraries to enrich genes of interest and allows unbiased quantification of the whole transcriptome.

Thomas, Marx et al. devise a live imaging approach to spatiotemporally dissect mouse ovulation ex vivo.

Dardano et al. generate human pluripotent stem cell-derived cardiac organoids capable of undergoing endothelial-to-haematopoietic transition and producing haematopoietic cells.

Dimitrov et al. present LIANA+, a framework that unifies and extends approaches to study inter- and intracellular signalling from diverse mediators, captured from single-cell, spatially resolved and multi-omics data.

Cao et al. describe the development and application of an engineered protein system (MARS) derived from PLEKHA5 that allows mitosis-specific recruitment of proteins to the plasma membrane to study protein function in cell division.

Hamazaki, Yang et al. report that an early pulse of retinoic acid robustly induces human gastruloids with a neural tube, segmented somites and more advanced cell types than conventional gastruloids.

Qin, Liu and colleagues develop a tool that combines CRISPR technology with G-quadruplex (G4)-stabilizing protein or ligand to specifically target DNA G4 structures. This tool provides better understanding of G4 functions and enables G4-based drug development.

Huang, Qin, Shang et al. profile double-strand breaks (DSBs) generated by C-to-G base editors (CGBEs) and find that HMCES protects abasic sites and reduces CGBE-triggered DSBs.

Noack and Vangelisti et al. present 3DRAM-seq, which simultaneously profiles genome organization, chromatin accessibility and DNA methylation at high resolution and allows mapping cell-type-specific epigenetic regulation in human neurogenesis.

Timms, Mena et al. present a multiplex CRISPR screening platform capable of assigning E3 ligases to their substrates and degrons at scale.

Huang et al. provide a method to generate human gastric stem cell-derived pancreatic islet-like organoids that are capable of restoring glucose homeostasis in diabetic mice.