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RNA-seq on ES cells where DDX6 was knocked down by the AID method

ABSTRACT: RNA-seq on ES cells where DDX6 was knocked down by the AID method

PROVIDER: PRJNA824800 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18685804.fastq.gz	Fastqsanger.gz
	SRR18685805.fastq.gz	Fastqsanger.gz
	SRR18685806.fastq.gz	Fastqsanger.gz
	SRR18685807.fastq.gz	Fastqsanger.gz
	SRR18685808.fastq.gz	Fastqsanger.gz

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RNA-seq on ES cells where DDX6 was knocked down by the AID method

Project description:To degrade DDX6 acutely, we adopted an advanced protein degradation method, the auxin-induced degron (AID) system. For this purpose, we prepared an AID-tagged DDX6 and E3 ligase subunit of OsTIR1 in an engineered ES (D6AdP cell line). These deposited data are RNA-seq data on these D6AdP ES cells treated with the auxin analog (IAA) treatment for 0, 3, and 6 hours.

2022-11-01 | GSE200483 | GEO

RNA-seq of coding RNA from DDX6 knockout human haploid (HAP1) cells

Project description:We performed a genome-scale screen for suppressors of interferon stimulated gene (ISG) expression in human haploid cells (HAP1). DEAD-box helicase 6 (DDX6) was a significant hit. In order to validate DDX6 as a regulator of ISG expression, we created knockouts of DDX6 in HAP1 cells using CRISPR-Cas9 and performed RNA-seq on coding RNA from DDX6 KO and WT cells. This data was used to determine if ISGs were upregulated in DDX6 KO HAP1 cells.

2017-07-25 | E-MTAB-5867 | biostudies-arrayexpress

mRNA transcriptome analyses of the functions of DDX6-mediated pathways during EpiLC induction

Project description:DDX6 is an RNA helicase and involved in various post-transcriptional regulatory processes. Although DDX6 is an evolutionarily well conserved central player in post-transcriptional gene regulation, its function in embryonic development remains obscure. In this study, we have identified the crucial functions of DDX6 during early mouse embryogenesis. However, due to its wide range of involvement, the more detailed dissection of DDX6-mediated functions was required to pinpoint which specific DDX6 function is important. For this purpose, we selected a key gene of each well-known DDX6 pathway, generated KO ES line, then made cDNA libraries of ESC and EpiLC Day2 samples to investigate transcriptomic differences during the very early differentiation processes of embryonic pluripotent cells.

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Expression data from knock-down ES stable cell line

Project description:In order to identify the effects of the knock-down of the gene of interest on the mouse ES transcriptome, we performed Affymetrix Gene-Chip hybridization experiments for the knock-down cell line. Transcriptome analysis of the knock-down transgenic mouse ES cell line. The knock-down cell line (shE13) was generated by stably expressing a specific short-hairpin RNA against E13 sequence thus knocking-down E13 expression in parental mouse ES cell line E14Tg2a.4 (E14, Hooper M et al., 1987). The specific mouse gene knocked down in the ES cell line is E130012A19Rik.

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Large-scale study of total and polysomial mRNA after DDX6 depletion in HEK293 cells

Project description:DDX6 is an abundant cytoplasmic DEAD-box RNA helicase which is involved in disparate aspects of mRNA stability and translation, leading to a confused understanding of its global function. We carried out a large-scale study of total and polysomial mRNA after DDX6 depletion to get an accurate picture of its roles in human cells.

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mRNA transcriptome analysis of Ddx6 knockout embryos

Project description:DDX6 is an RNA helicase and involved in various post-transcriptional regulatory processes. Although DDX6 is an evolutionarily well conserved central player in post-transcriptional gene regulation, its function in embryonic development remains obscure. To study this, we examined Ddx6 knockout mouse embryos and pluripotent cell lines. E8.5 Ddx6 mutants exhibited gastrulation defects. To transcriptomically identify the existing cell population in E8.5 mutant embryos and further find the possible causes of this defect, we performed RNA-seq analysis with E8.5 embryo cDNA libraries.

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Expression data from knock-down ES stable cell line

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The RNA helicase DDX6 regulation in human skeletal myoblasts [eCLIP-seq]

Project description:Analysis of DDX6 eCLIP in human skeletal myoblasts to identify DDX6 target genes, and binding locations.

2019-10-16 | GSE125809 | GEO

Human DDX6 regulates translation and decay of inefficiently translated mRNAs

Project description:Recent findings indicate that the translation elongation rate influences mRNA stability. One of the factors that has been implicated in this link between mRNA decay and translation speed is the yeast DEAD-box helicase Dhh1p. Here, we demonstrate that the human ortholog of Dhh1p, DDX6, triggers deadenylation-dependent decay of inefficiently translated mRNAs in human cells. DDX6 interacts with the ribosome through the Phe-Asp-Phe (FDF) motif in its RecA2 domain. Furthermore, RecA2-mediated interactions and ATPase activity are both required for DDX6 to destabilize inefficiently translated mRNAs. Using ribosome profiling and RNA sequencing, we identified two classes of endogenous mRNAs that are regulated in a DDX6-dependent manner. The identified targets are either translationally regulated or regulated at the steady-state-level and either exhibit signatures of poor overall translation or of locally reduced ribosome translocation rates. Transferring the identified sequence stretches into a reporter mRNA caused translation- and DDX6-dependent degradation of the reporter mRNA. In summary, these results identify DDX6 as a crucial regulator of mRNA translation and decay triggered by slow ribosome movement and provide insights into the mechanism by which DDX6 destabilizes inefficiently translated mRNAs.

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