Spatial Transcriptome (ST) technologies are emerging as powerful tools for studying tumor biology. However, existing tools for analyzing ST data are limited, as they mainly rely on algorithms developed for single-cell RNA sequencing (scRNAseq) data and do not fully utilize the spatial information. While some algorithms have been developed for ST data, they are often designed for specific tasks, lacking a comprehensive analytical framework for leveraging spatial information.
In this study, we present StereoSiTE, an analytical framework that combines open-source bioinformatics tools with custom algorithms to accurately infer the functional Spatial Cell Interaction Intensity (SCII) within the Cellular Neighborhood (CN) of interest. We applied StereoSiTE to decode ST datasets from xenograft models and found that the CN efficiently distinguished different cellular contexts, while the SCII analysis provided more precise insights into intercellular interactions by incorporating spatial information. By applying StereoSiTE to multiple samples, we successfully identified a CN region dominated by neutrophils, suggesting their potential role in remodeling the immune Tumor MicroEnvironment (iTME) after treatment. Moreover, the SCII analysis within the CN region revealed neutrophil-mediated communication, supported by pathway enrichment, transcription factor regulon activities, and protein-protein interactions.
StereoSiTE represents a promising framework for unraveling the mechanisms underlying treatment response within the iTME by leveraging CN-based tissue domain identification and SCII-inferred spatial intercellular interactions. The software is designed to be scalable, modular, and user-friendly, making it accessible to a wide range of researchers.

Primer sequences. (XLSX 8 kb)

Primer sequences. (XLSX 8 kb)

No description available

Table S1. The primer and siRNA sequence.

Table S1. The primer and siRNA sequence.

The domestic goat is one of the most important livestock species in the world, especially in China, India and other developing countries. Goats not only serve as an important source of meat, milk, fiber and pelts, and have fulfilled agricultural, economic, cultural and even religious roles from very early times in human civilization, but also are now used as animal models for biomedical research and transgene production of protein medicines.We would like to share all the genome data of goat. We hope the genome sequence of goat can provide a new resource for biological research and breeding of goat and other small ruminants.
We sequenced the 2.92 Gb genome to a depth of approximately 65.6 X with short reads from a series of libraries with various insert sizes ( 170 bp, 350 bp, 800 bp, 2 kb, 5 kb, 10 kb and 20 kb) on a HiSeq 2000 sequencer.
The assembled scaffolds of high quality sequences total 191.5 Gb, with the contig and scaffold N50 values of 18.7 kb and 2.21 Mb respectively. We identified 22,175 protein-coding genes.In addition, we also provide the restriction-enzyme fragment maps derived from the whole genome mapping (WGM) technology developed by the Argus System (method described in this paper).
Scaffolds derived from de novo assembly of next-generation sequencing data are converted into restriction maps by in silico restriction enzyme digestion. Then, the distance between restriction enzyme sites in the sequencing-derived scaffolds are matched to the lengths of the optical fragments in the single-molecule WGM restriction maps. Matches allow the scaffolds to be extended and linked into super-scaffolds.

Foxtail millet (Setaria italica) (2n=18), is an annual grass grown both as cereal crop (grain production) and as forage food. It is primarily grown in temperate, subtropical and tropical areas. With approximately 6,000 varieties, millet is one member of the Panicoideae (grasses subfamily), which includes maize (Zea mays), sorghum (Sorghum bicolor), and sugar cane (Saccharum officinarum). It is a nutritious dietary staple, containing starch, proteins, and a number of vitamins and minerals, such as calcium, iron, and sodium. It feeds nearly one-third of the world population with main daily-calories intake, and is especially prevalent in dry climates or soil-poor regions that are not suited for the cultivation of many other crops. Millet is self-pollinating, has a short lifecycle, is small in stature, and has a small genome size; all of these useful attributes make it an invaluable functional genomics model system, and an excellent reference genome to aid in the sequencing of other larger grasses genomes.

Chinese hamster ovary (CHO) K1 cells are a cell line cultured from the ovary of the Chinese hamster (Cricetulus griseus). CHO cells are often used in biological and medical studies and commercially in the production of therapeutic proteins, which contribute significantly to the $100 billion biopharmaceutical market.BGI sequenced the CHO K1 genome genome using next-generation sequencing technology, assembling a 2.45G genome with 24,383 predicted genes.