DescriptionRNA-binding profiles of Hspa1b as an RNA-binding protein in the mouse hippocampus
OEP005267
DescriptionAmplicon and metagenomic datasets of two representative iron mines in the Panxi Mining Area, Southwest China
OEP005245
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
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