DescriptionRNA-seq of photorespiratory bypass plants
Used IDNODEP00000033  
OEP000073 Public
DescriptionSplicing dysregulations extensively occur in cancers, yet the biological consequences of such alterations are mostly undefined. Here we report that the Hippo-YAP signaling, a key pathway that regulates cell proliferation and organ size, is under control of a new splicing switch. We show that TEAD4, the transcription factor that mediates Hippo-YAP signaling, undergoes alternative splicing facilitated by the tumor suppressor RBM4, producing a truncated isoform, TEAD4-S, which lacks N-terminal DNA-binding domain but maintains YAP-interaction domain. TEAD4-S is located in both nucleus and cytoplasm, acting as a dominant negative isoform to YAP activity. Consistently, TEAD4-S is reduced in cancer cells, and its re-expression suppresses cancer cell proliferation and migration, inhibiting tumor growth in xenograft mouse model. Furthermore, TEAD4-S is reduced in human cancers, and patients with elevated TEAD4-S levels have improved survival. Altogether these data reveal a novel RBM4-mediated splicing switch that serves to fine-tune Hippo-YAP pathway.
Used IDNODEP00000038  
OEP000074 Public
DescriptionThis data set contain NGS raw data (fastQ) of 77 samples.
Used IDNODEP00000039  
OEP000075 Public
DescriptionWe used time series RNA-seq data collected from etiolated maize and rice leaf tissues sampled during a greening process to systematically characterize the differences and conservations of gene expression patterns between the two species.
Used IDNODEP00000040  
OEP000076 Public
DescriptionProgression through the mitotic cell cycle requires periodic regulation of gene function at the levels of transcription, translation, protein-protein interactions, post-translational modification and degradation. However, the role of alternative splicing (AS) in the temporal control of cell cycle is not well understood. By sequencing the human transcriptome through two continuous cell cycles, we identify ~1,300 genes with cell cycle-dependent AS changes. These genes are significantly enriched in functions linked to cell cycle control, yet they do not significantly overlap genes subject to periodic changes in steady-state transcript levels. Many of the periodically spliced genes are controlled by the SR protein kinase CLK1, whose level undergoes cell cycle-dependent fluctuations via an auto-inhibitory circuit. Disruption of CLK1 causes pleiotropic cell cycle defects and loss of proliferation, whereas CLK1 over-expression is associated with various cancers. These results thus reveal a large program of CLK1-regulated periodic AS intimately associated with cell cycle control.
Used IDNODEP00000042  
OEP000077 Public
Descriptioncirc_as
Used IDNODEP00000045  
OEP000080 Public
DescriptionWe collected embryos from early-to-later of 8 chordate species and did RNA high-throughput sequencing to identify the expression profile for each species across the developmental process. To identify the conserved and divergent expression profile across chordates and to understand the developmental mechanism through the evolutionary history
Used IDNODEP00000046  
OEP000081 Public
DescriptionWe have used RNA-seq to examine circular RNAs from poly(A)-/ribo- RNAs in human and mouse embryonic stem cells
Used IDNODEP00000050  
OEP000082 Public
DescriptionWe have optimized the metabolic tagging of newly transcribed RNAs by 4-thiouridine (4sU) to identify newly-transcribed (nascent) circRNAs from human PA1 cells, undifferentiated H9 cells and H9 differentiated FB neurons.
Used IDNODEP00000051  
OEP000083 Public
Description16S data of Han, KZK and UIG
Used IDNODEP00000052  
OEP000084 Public