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DHX9 suppresses spurious RNA processing defects originating from the Alu invasion of the human genome [RNA-Seq]

GSE85161 Homo sapiens Expression profiling by high throughput sequencing 24 samples Submitted 2017/03/28 Platform GPL18573
Summary
Transposable elements increase genetic diversity thus making them an important part of evolution and gene regulation in all organisms that carry these sequences. Bulk of our nascent transcriptome is comprised of transposable elements that have the propensity to form strong secondary structures. It is essential to resolve such strong secondary structures to maintain normal cellular function. Here, we show that the major nuclear RNA helicase DHX9/RHA interacts and remodels embedded Alu retrotransposable elements in the human transcriptome and B1 retrotransposable elements in the mouse transcriptome. To understand the effect of loss of DHX9 in human transcriptome we performed knockdown of DHX9 in HEK293 cells using two different siRNAs, followed by polyA-plus and polyA minus RNA extraction and sequencing.
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Direct links to NCBI, no account and no request form: the whole study as GSE85161_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 24 samples. Raw sequencing reads are also available from ENA.

Also filed as BioProject PRJNA336449 and SRA study SRP080966. Searching any of these in the dataset finder brings you back here.

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