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  • PROJ Glacier forefield metagenome and metatranscriptome study

    Mukan Ji, Lanzhou University,2024.07.07

    Description

    This project investigates the microbial community function changes in the recently exposed glacier forefields with ecosystem succession using both metagenome and metatranscriptome

    OEP005447

  • PROJ XM_S_16S

    Zheng Lab, Fudan univerisity,2023.05.04

    Description

    OEP004135

  • PROJ 3D facial landmark meta-analysis

    Siyuan Du, Shanghai Institute of Nutrition and Health, CAS,2024.07.03

    Description

    Facial morphology, a complex trait influenced by genetics, holds great significance in evolutionary research. However, due to limited fossil evidence, the facial characteristics of Neanderthals and Denisovans have remained largely unknown. In this study, we conducted a large-scale multi-ethnic meta-analysis of Genome-Wide Association Study (GWAS), including 9,764 East Asians and 10,115 Europeans, quantitatively assessing 78 facial traits using 3D facial images. We identified 71 genomic loci associated with facial features, including 21 novel loci.

    OEP005438

  • PROJ CircRREB1 concatenates metabolic reprogramming and stemness maintenance to facilitate pancreatic ductal adenocarcinoma progression

    Zeyin Rong, Fudan University Shanghai Cancer Center,2024.07.05

    Description

    1. CircRNA sequencing was performed to analyse 7 primary pancreatic ductal adenocarcinoma(PDAC) tissues (including 4 PDAC tissues with a lower SUVmax and 3 PDAC tissues with a higher SUVmax). 2. CircRNA sequencing was performed to analyse in 8 primary PDAC tissues (including 4 tumour-node-metastasis (TNM) stage I PDAC tissues and 4 TNM stage VI PDAC tissues). 3. RNA-seq to detect differentially expressed genes (DEGs) between Capan-1 cells with circRREB1 knockdown (sh-circRREB1) and control cells (sh-NC).

    OEP005444

  • PROJ Toward best practices for detecting germline small variants: a large-scale real-world WES benchmarking study using the Quartet DNA reference materials

    Ying Yu, Fudan University,2024.07.04

    Description

    Whole-exome sequencing (WES) plays a crucial role in diagnosing genetic diseases by identifying germline variants. However, reproducibility issues limit its clinical utility. We conducted a large-scale proficiency test across 89 clinical and commercial labs in China, employing the well-characterized Quartet DNA reference materials, to evaluate the impact of experimental and bioinformatic factors on the performance of small variant detection. We observed significant variability in sequencing data quality and variant calling performance, with higher raw read quality and lower contamination levels improved variant detection. Our findings emphasized the collective influence of multiple factors on variant detection, with capture efficiency metrics, such as fold-80 penalty, on-target rate, and target region coverage, instead of base-by-base quality metrics on raw sequences, emerging as the most critical. Our study not only revealed the nationwide performance of WES in China, but also provided actionable best practices for optimizing the entire WES process, from data generation to analysis, thereby enhancing variant detection quality and reliability.

    OEP005441

  • PROJ CircRREB1 concatenates metabolic reprogramming and stemness maintenance to facilitate pancreatic ductal adenocarcinoma progression

    ZI JIAN, ,2024.07.04

    Description

    CircRNA sequencing was performed to analyse 7 primary PDAC tissues (including 4 PDAC tissues with a lower SUVmax and 3 PDAC tissues with a higher SUVmax)

    OEP005442

  • PROJ Proteomics and metabolomics data of NSPT cohort

    Wenran Li, ,2024.07.04

    Description

    Samples in the NSPT cohort included 3,557 Chinese individuals recruited as volunteers from three regional districts in China: Zhengzhou, Taizhou, and Nanning. For each individual, we conducted comprehensive omics profiling of 12,882 plasma proteins and 351 serum metabolites in blood tissue.

    OEP005440

  • PROJ Serum and tissue microbiome (2bRAD-M sequencing) of CRC

    Lu Zhao, Weifang People's Hospital,2023.03.16

    Description

    This project is the investigation of the characteristics of serum and tissue microbiota between CRC patients using 2bRAD-M gene sequencing.

    OEP004048

  • PROJ Reactive iron as an important reservoir of marine organic carbon over geological timescales

    sui weikang, shanghai jiaotong univerisity,2023.07.16

    Description

    Reactive iron (FeR) has been suggested to serve as a semi-persistent sink of organic carbon (OC) in surface marine sediments, where approximately 10-20% of total OC (TOC) is associated with FeR (FeR-OC). However, the persistence of FeR-OC on geological timescales remains poorly constrained. Here, we retrieved FeR-OC records in two long sediment cores of the northern South China Sea spanning almost the past 100 kyrs. Most prominently, the downcore marine-sourced FeR-OC contributes a relative stable proportion of 13.3±3.2% to TOC. However, distinctly lower values of less than 5% of TOC, accompanied by notable 13C depletion of FeR-OC are observed in the sulfate-methane transition zone (SMTZ), where active sulfate reduction and potential iron reduction are indicated by microbial composition and geochemical modelling. FeR-OC is suggested to be remobilized by abiotic and biotic reductive dissolution of FeR (and might be substituted with freshly formed 13C-depleted OC). The global budget of FeR-OC in marine sediments influenced by microbial processes could be as large as 312±126×1017 g, which is 21-50 times the size of the atmospheric carbon pool. Thus, sedimentary FeR-OC as an exchangeable reservoir of labile OC may support deep life and play a role in regulating Earth’s carbon cycle over geological timescales.

    OEP004265

  • PROJ FITC-ID

    Xinwen Yan, ,2024.07.02

    Description

    OEP005436