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  • PROJ ECS based on NGS in Southern Chinese couples

    Lanchun Gu, Fulgent,2024.05.10

    Description

    Comprehensive expanded carrier screening using next-generation sequencing in Southern Chinese couples

    OEP005278

  • PROJ Analysis of blood methylation quantitative trait loci in East Asians identifies ancestry-specific effects associated with complex trait variation

    Sijia Wang, Shanghai Institute of Nutrition and Health,Chinese Academy of Sciences,2021.11.16

    Description

    This project has included individual-level genotype data (SNP chip, methy_3523_qc0.01.bed,bim,fam) and DNA methylation data (Illumina EPIC, methy_3523.rdata) of 3523 Han Chinese (NSPT), and also the individual-level genotype data (SNP chip, 200505_960Sps_passed.vcf) and DNAm data (Illumina EPIC, beta_norm.rda) of additional 798 individuals (CGZ), which are in controlled access. The individual-level genotype data is not available because of IRB restriction due to privacy concern. The individual-level DNA methylation data can be available with reasonable requests. The project also included mQTL summary statistics (cis1_10.zip, cis11_22.zip, lcis.zip, trans.zip) with threshold of 1e-10 in 3523 Han Chinese (NSPT), SNP information (effect allele equals to minor allele, and effect allele frequency) in NSPT (snp_chr1_22.info.zip), the replication for these mQTLs (CGZ_mQTL.rep2.csv) in the CGZ cohort, and blood cell-lineage (lymphoid- and myeloid-) mQTLs estimated by using CELLDMC (cts_mQTL_info.Rd). These data are available for download. Data usage shall be in full compliance with the Regulations on Management of Human Genetic Resources in China. Use of this data requires a citation of our article. For controlled access data, requests are normally processed within two weeks. A template of the data sharing and confidentiality agreement will be sent to the applicant, and the data can be used within the permitted scope after the data sharing and confidentiality agreement has been signed.

    OEP002902

  • PROJ Hspa1b

    Xiaofeng Zhao, The First Affiliated Hospital of Zhengzhou University,2024.05.09

    Description

    RNA-binding profiles of Hspa1b as an RNA-binding protein in the mouse hippocampus

    OEP005267

  • PROJ Native microbial populations in the alkaline mines in Panxi Area, Southwest China

    Yu He, China University of Geosciences (Wuhan),2024.04.28

    Description

    Amplicon and metagenomic datasets of two representative iron mines in the Panxi Mining Area, Southwest China

    OEP005245

  • PROJ Cross-feeding interactions among the major degrader and rare non-degraders in a bacterial consortium reveal the role of bacterial dark matter in lignin degradation

    Qiannan Peng, Shandng University,2023.12.26

    Description

    Lignin is the abundant aromatic carbon polymer on earth. Its bioconversion is essential in global carbon cycle and bioenergy production. Microbial communities, which have evolved versatile enzymes and pathways, undoubtedly play a vital role in lignin biodegradation. The interactions among members in a community greatly affect the performance outcome, yet it's a significant challenge to mechanistically unravel such complex interactions. In this study, we developed the marine lignin degrading bacterial consortium (LD), through “top-down” enrichment. 16s rRNA amplicon sequencing revealed that LD is dominated by Pluralibacter gergoviae (> 98%), a lignin degrader. Further physiological analysis demonstrated that the additional unaddressed members, as the dark matter, hidden behind P. gergoviae to promote growth and lignin degradation. Genome-scale metabolic models were constructed for P. gergoviae and three non-lignin degrading species, which represent the top four members in LD consortium. The integrated in silico simulation predicted that growth/degradation is boosted by metabolic exchanges between members and enable us to construct the “bottom-up” four-species synthetic community. The performance of synthetic consortia validated the predication and revealed that the non-degraders survived on metabolic intermediates from P. gergoviae, including succinate, malate, serine and PCA derivates. In return, the non-degraders fed back glycerol, aspartate, alanine, fumarate to P. gergoviae to stimulate growth and further enhance lignin degradation. Our study uncovered the black-box of LD consortium, in which the dark matter interacts to form a syntrophy with P. gergoviae for lignin catabolism. Also, it provided a valuable step forward in manipulating microbiomes for biotechnology development.

    OEP004885

  • PROJ Diversity of microbial communities in Zhoushan

    Kai Tang, Xiamen University,2023.03.14

    Description

    OEP004024

  • PROJ The Proteogenomic Landscape of pancreatic ductal adenocarcinoma

    yunguang Li, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences,2024.01.08

    Description

    We collected pancreatic cancer samples by surgery palliative operation ascites or endoscopic ultrasound-guided fine-needle aspiration biopsy (EUS-FNA) and generated a PDPCOs cohort with whole-genome sequencing (WGS), RNA sequencing (RNA-seq), the assay for transposase-accessible chromatin using the sequencing (ATAC-seq), proteomics, phospho-proteomics, glyco-proteomics, drug sensitivities (targeted agents and chemotherapeutic drugs) and radiation sensitivity.

    OEP004966

  • PROJ Altered nucleocytoplasmic export of adenosine (A)-rich circRNAs by PABPC1 contributes to neuronal function

    Li Yang, Fudan University,2024.04.27

    Description

    Circular RNAs (circRNAs) are upregulated during neurogenesis. Where and how circRNAs are localized, and what roles they play during this process have remained elusive. By comparing the nuclear and cytoplasmic circRNAs between H9 cells and H9-derived forebrain neurons (FB), we found a subset of adenosine (A)-rich circRNAs are restricted in H9 nuclei but exported to cytosols upon forebrain neuron differentiation. This differentiation-coupled circRNA subcellular relocation is modulated by the poly(A)-binding protein PABPC1. In the nucleus, newly produced (A)-rich circRNAs are bound by PABPC1 and the nuclear basket protein TPR to prevent their nucleocytoplasmic export. Modulation of (A)-rich motifs in circRNAs remarkably alters their subcellular localization. Enforced (A)-rich circRNAs in cytosols result in mRNA translation suppression. Furthermore, decreased nuclear PABPC1 upon neuronal differentiation enables the export of (A)-rich circRNAs including circRTN4(2,3), which is required for neurite outgrowth. These findings uncover subcellular localization features of circRNAs, linking their processing and function during neurogenesis.

    OEP005241

  • PROJ 20240430_WGBS

    GuLan chun, Fulgent,2024.04.29

    Description

    20240430_WGBS

    OEP005253

  • PROJ 20240429_WGBS

    GuLan chun, Fulgent,2024.04.29

    Description

    OEP005251