RNA-seq of KD, rescues of NMD factors, and UPF1-flag CLIP-seq in HeLa cells.
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.
Provenance — who produced it, who reused it
Linked to 11 papers in the literature. Roles are inferred factual signals (who deposited the data vs who reused it), with counts — never a judgement about any author.
- Structure-Mediated RNA Decay by UPF1 and G3BP1 2020 · 282 cites
- Predictive models of subcellular localization of long RNAs 2019 · 118 cites
- SMG5-SMG7 authorize nonsense-mediated mRNA decay by enabling SMG... 2021 · 106 cites
- Exon Junction Complex Shapes the Transcriptome by Repressing Rec... 2018 · 100 cites
- Identification and analysis of ribosome-associated lncRNAs using... 2018 · 83 cites
5 further papers cite this accession but reuse could not be confirmed.
Deep data QC
metadata only · no data-level QC for this typeStandardized, field-standard QC computed by touching the data — every metric states how it was obtained
No quantitative QC rubric exists for this data type yet, so it is deliberately left unscored — this is an honest "not applicable", not a poor rating.
measured = computed from the data · extrapolated/reported = derived or from the repository · dq-1.0 · provisional — verify independently