Jiawei CHEN, HKUST,2023.02.28

Description

Clean reads from RNA-seq duplicates were trimmed using Trimmomatic v0.39 and then de-novo co-assembled using Trinity v2.14.0. Similar transcripts were clustered using CD-HIT with ‘-c 0.95’ parameter, and a single representative transcript was retained for each group. The quality of transcriptomic assembly was estimated using BUSCO v5.4.4 with the lineage dataset ‘alveolata_odb10’ (C:98.8%[S:26.3%,D:72.5%],F:0.6%,M:0.6%,n:171).

OEP003883

Jin Zeng, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences,2023.07.27

Description

Rhizosphere soil, bulk soil, and sediment samples from lakeshore wetlands in Tibetan Plateau

OEP004316

Zheng Lab, Fudan univerisity,2024.05.06

Description

Ketogenic diet-induced bile acids protect against obesity through reduced calorie absorption

OEP005260

Xin Li, Shanghai Institute of Nutrition and Health,CAS,2023.01.03

Description

To distinguish aggressive prostate cancer at early disease stages is essential for personalized treatment. Here we explore the correlation of prostatic HSD3B1 activity with tumor aggressiveness to generate genomic classifiers for patient stratification and investigate mechanisms for patient metabolic heterogeneity to accelerate HSD3B1-based disease prevention and treatment. Patient prostatic HSD3B1 activity was evaluated by tracing [3H]-labeled androgen metabolism in fresh prostatic biopsies ex vivo. Potent prostatic HSD3B1 activity were more frequently found in patients with metastatic disease or worse treatment response, but less frequently found in finasteride-treated patients. Germline genetic variations and somatic mutations associated with prostatic HSD3B1 activity were evaluated. A gene signature reflecting transcriptome features of potent prostatic HSD3B1 activity was also generated as a clinic-accessible approach for patient stratification. UBE3D was found to be associated with metabolic heterogeneity, as an ubiquitin ligase regulating HSD3B1 homeostasis. Equilin was discovered as a potent HSD3B1 antagonist and inhibited tumor growth after UBE3D knockout, providing potential promising strategy for the prevention and early treatment of aggressive prostate cancer. Overall, our findings indicate that prostatic HSD3B1 activity is correlated with tumor aggressiveness at early disease stages and HSD3B1 is both a predictive biomarker but also a therapeutic target for aggressive prostate cancer.

OEP003830

Peng Xing, Nanjing Institute of Geography & Limnology, Chinese Academy of Sciences,2023.05.16

Description

Structure and function of lake microbiomes on the Tibetan Plateau

OEP004147

Min Shao, Chinese acadmey of sciences,2024.04.09

Description

OEP005190

QL Q, SINH, CAS,2024.06.06

Description

OEP005375

Jin Zeng, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences,2021.09.16

Description

Aquatic plant associated samples collected from natural field sites.

OEP002727

Guangdun Peng, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences,2024.06.03

Description

The functional development of the mammalian lung is a complex process that relies on the spatial and temporal organization of multiple cell types and their states. However, a comprehensive spatiotemporal transcriptome atlas of the developing lung has yet to be reported. Here we apply high-throughput spatial transcriptomics to allow for a comprehensive assessment of mouse lung development comprised of two important developmental events: branching morphogenesis and alveolar formation. We firstly generate a spatial molecular atlas of mouse lung development spanning from E12.5 to P0 based on integration of published single-cell RNA-sequencing data and identify 10 spatial domains critical for functional lung organization. We observe the establishment of pulmonary airways within the developing lung, accompanied by the proximal-distal patterning by distinct characteristics of gene expression, signaling restriction and transcription factors enrichment. We introduce the alveolar niche heterogeneity with maturation state differences during the later developmental stage around birth and demonstrate differentially expressed genes, such as Angpt2 and Epha3, which may perform a critical role during alveologenesis. In addition, multiple signaling pathways, including ANGPT, VEGF and EPHA, exhibit increased enrichment in more maturing alveolar niche. Furthermore, we create a lineages map connecting spatial domains from adjacent time points in E12.5-P0 lungs and explore TF regulatory networks specific for each lineage.

OEP005365

Quanrui Chen, ,2024.05.29

Description

The global increase in hypoxic zones necessitates a comprehensive understanding of marine organic carbon cycling dynamics under hypoxic conditions to evaluate their impact on global carbon cycles and ecosystem health. This study, conducted in the seasonal hypoxia zone of the Yangtze River Estuary, investigates the effects of deoxygenation on the microbial utilization of algal-derived organic carbon. Through culture experiments and molecular analyses, the research explores the adaptability of heterotrophic bacterial communities in response to hypoxia, focusing on changes in composition and metabolic pathways. High-throughput 16S rDNA sequencing is used to analyze shifts in microbial community dynamics and their role in organic carbon transformation. The study aims to provide new insights into the complex interactions between microbial communities and organic matter cycling under hypoxic conditions, informing strategies for managing marine ecosystems amidst global change.

OEP005359