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Accession IconSRP090954

RESA identifies mRNA regulatory sequences with high resolution

Organism Icon Danio rerio
Sample Icon 23 Downloadable Samples
Technology Badge IconIllumina HiSeq 2000

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Description
Gene expression is regulated extensively at the level of mRNA stability, localization, and translation. However, decoding functional RNA regulatory features remains a limitation to understanding post-transcriptional regulation in vivo. Here, we developed RNA Element Selection Assay (RESA), a method that selects RNA elements based on their activity in vivo and uses high-throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements, we developed a bisulfite-mediated nucleotide conversion strategy for large-scale mutational analysis (RESA-bisulfite). Finally, we used the versatile RESA platform to map candidate protein-RNA interactions in vivo (RESA-CLIP). The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.
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Total Samples
23
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RESA-Seq - Needle r2
NA
RESA-Seq - Mut 64c B1
NA
RESA-Seq - Mut 64c B2
NA
RESA-Seq - Mut 64c B2
NA
RESA-Seq - Mut 64c B3
NA
RESA-Seq - Mut 8h B3
NA
RESA-CLIP Ago2 - RESA-CLIP Ago2 input
NA
RESA-Seq - Mut 64c B3
NA
RESA-Seq - Mut 8h B1
NA
RESA-Seq - WT 64c pA r3 B1
NA
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