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Stereo-seq V2: Spatial mapping of total RNA on FFPE sections with high resolution

Stereo-seq V2 facilitates single-cell-resolution spatial RNA mapping in FFPE samples through random primer capture, uncovering ncRNAs, host-pathogen transcriptome profiling, and spatial immune repertoires in situ.

OpenS2S: Advancing Fully Open-Source End-to-End Empathetic Large Speech Language Model

arXiv:2507.05177v3 Announce Type: replace-cross Abstract: Empathetic interaction is a cornerstone of human-machine communication, due to the need for understanding speech enriched with paralinguistic cues and generating emotional and expressive responses. However, the most powerful empathetic LSLMs are increasingly closed off, leaving the crucial details about the architecture, data and development opaque to researchers. Given the critical need for transparent research into the LSLMs and empathetic behavior, we present OpenS2S, a fully open-source, transparent and end-to-end LSLM designed to enable empathetic speech interactions. Based on our empathetic speech-to-text model BLSP-Emo, OpenS2S further employs a streaming interleaved decoding architecture to achieve low-latency speech generation. To facilitate end-to-end training, OpenS2S incorporates an automated data construction pipeline that synthesizes diverse, high-quality empathetic speech dialogues at low cost. By leveraging large language models to generate empathetic content and controllable text-to-speech systems to introduce speaker and emotional variation, we construct a scalable training corpus with rich paralinguistic diversity and minimal human supervision. We release the fully open-source OpenS2S model, including the dataset, model weights, pre-training and fine-tuning codes, to empower the broader research community and accelerate innovation in empathetic speech systems. The project webpage can be accessed at https://casia-lm.github.io/OpenS2S

Stereo-seq V2: Spatial mapping of total RNA on FFPE sections with high resolution

Cell. 2025 Aug 22:S0092-8674(25)00922-5. doi: 10.1016/j.cell.2025.08.008. Online ahead of print.

ABSTRACT

Performing total RNA profiling on formalin-fixed, paraffin-embedded (FFPE) samples, the predominant sample conservation method in clinical practice, remains challenging for current spatial transcriptomics techniques. Here, we introduce Stereo-seq V2, which employs random primers to capture and sequence RNAs in situ on FFPE sections and provides single-cell resolution. The random-priming-based strategy offers unbiased transcript capturing and uniform gene body coverage, which increase the sensitivity to marker genes, the efficiency of non-polyadenylation (poly(A)) RNA profiling, and immune repertoire coverage. We demonstrated the robust performance of Stereo-seq V2 on clinical FFPE samples using triple-negative breast cancer (TNBC) sections and identified tumor-specific alternative splicing events. In a Mycobacterium tuberculosis (Mtb)-infected mouse model, we monitored gene expression dynamics of host and pathogen transcriptomes simultaneously by utilizing Stereo-seq V2. We also assembled immune repertoires and identified Mtb-specific BCR clones, which could also be observed in human tuberculous lung samples. These results highlight Stereo-seq V2's potential in biomedical research and personalized medicine.

PMID:40882628 | DOI:10.1016/j.cell.2025.08.008

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