DescriptionLignin 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
DescriptionKetogenic diet-induced bile acids protect against obesity through reduced calorie absorption
OEP005260
DescriptionThis 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), 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
Description
OEP004024
DescriptionWe 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
DescriptionCircular 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
Description20240430_WGBS
OEP005253
Description
OEP005251
DescriptionThese are 16S rDNA sequences predicted from metagenomic reads, used for overall analysis of the prokaryotic community structure, diversity in aquatic environments, its relationship with seawater depth, and the variation of gene relative abundance with seawater depth.
OEP005246
Description20240428_WGS
OEP005243