Transcriptomics,Genomics

Dataset Information

155

RNA-seq of KD, rescues of NMD factors, and UPF1-flag CLIP-seq in HeLa cells.


ABSTRACT: This study aims at confidently identifying endogenous nonsense mediated decay (NMD) targets. To achieve this purpose, we performed KD of a few NMD factors in HeLa cells. Additionally, we performed rescue experiments for each factor, expressing an RNAi-resistant version of the gene from a plasmid. To determine transcripts bound by UPF1 in HeLa cells, A construct with a C-terminally flag tagged version of UPF1 was expressed. In order to avoid competition with endogenous UPF1, a KD was performed. Overall design: KD and rescue of three NMD factors (UPF1, SMG6, SMG7), plus a combined SMG6 and SMG7 KD, with individual rescues. 2 biological replicates of UPF1-flag CLIP-seq were carried out.

INSTRUMENT(S): Illumina HiSeq 2500 (Homo sapiens)

SUBMITTER: Oliver Muehlemann 

PROVIDER: GSE86148 | GEO | 2016-12-19

SECONDARY ACCESSION(S): PRJNA340370

REPOSITORIES: GEO

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Publications

Transcriptome-wide identification of NMD-targeted human mRNAs reveals extensive redundancy between SMG6- and SMG7-mediated degradation pathways.

Colombo Martino M   Karousis Evangelos D ED   Bourquin Joël J   Bruggmann Rémy R   Mühlemann Oliver O  

RNA (New York, N.Y.) 20161118 2


Besides degrading aberrant mRNAs that harbor a premature translation termination codon (PTC), nonsense-mediated mRNA decay (NMD) also targets many seemingly "normal" mRNAs that encode for full-length proteins. To identify a bona fide set of such endogenous NMD targets in human cells, we applied a meta-analysis approach in which we combined transcriptome profiling of knockdowns and rescues of the three NMD factors UPF1, SMG6, and SMG7. We provide evidence that this combinatorial approach identifi  ...[more]

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