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  • PROJ RNA-seq of photorespiratory bypass plants

    Changpeng Xin, PICB,2016.04.20

    Description

    RNA-seq of photorespiratory bypass plants

    Used ID

    NODEP00000033  

    OEP000073 Public

  • PROJ A splicing switch of TEAD4 regulates Hippo-YAP signaling pathway to inhibit tumor proliferation

    Xiaojuan Fan, PICB,2016.05.03

    Description

    Splicing 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 ID

    NODEP00000038  

    OEP000074 Public

  • PROJ NGS data for TIB project

    Shuhua Xu, PICB,2016.05.03

    Description

    This data set contain NGS raw data (fastQ) of 77 samples.

    Used ID

    NODEP00000039  

    OEP000075 Public

  • PROJ Time series RNA-seq data of greening process of etiolated maize and rice leaf tissues

    Guangyong Zheng, PICB,2016.05.04

    Description

    We 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 ID

    NODEP00000040  

    OEP000076 Public

  • PROJ An extensive program of periodic alternative splicing linked to cell cycle progression

    Xiaojuan Fan, PICB,2016.05.20

    Description

    Progression 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 ID

    NODEP00000042  

    OEP000077 Public

  • PROJ CPDR Project

    Hong Li, PICB,2016.06.13

    Description

    CPDR AA/CA WGS and RNA-seq data; all the data is in aligned BAM format.

    Used ID

    NODEP00000043  

    OEP000078 Public

  • PROJ circ_as

    Xiaoou Zhang, PICB,2016.06.17

    Description

    circ_as

    Used ID

    NODEP00000045  

    OEP000080 Public

  • PROJ Transcriptome analysis on chordate embryo development

    Song Guo, PICB,2016.06.20

    Description

    We 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 ID

    NODEP00000046  

    OEP000081 Public

  • PROJ RNA-seq of poly(A)-/ribo- or poly(A)+ RNAs from human and mouse ES cells

    Changpeng Xin, PICB,2016.09.13

    Description

    We have used RNA-seq to examine circular RNAs from poly(A)-/ribo- RNAs in human and mouse embryonic stem cells

    Used ID

    NODEP00000050  

    OEP000082 Public

  • PROJ 4sUDRB-seq of human PA1 cells, undifferentiated H9 cells and H9 differentiated FB neurons.

    Changpeng Xin, PICB,2016.09.14

    Description

    We 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 ID

    NODEP00000051  

    OEP000083 Public