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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 19, 2016 |
| Title |
RNA-seq of KD, rescues of NMD factors, and UPF1-flag CLIP-seq in HeLa cells. |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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.
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| 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.
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| Contributor(s) |
Colombo M, Karousis ED, Mühlemann O |
| Citation(s) |
27864472, 34389041 |
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| Submission date |
Aug 28, 2016 |
| Last update date |
Aug 24, 2021 |
| Contact name |
Oliver Muehlemann |
| Organization name |
University of Bern
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| Street address |
Freiestrasse 6
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| City |
Bern |
| ZIP/Postal code |
3012 |
| Country |
Switzerland |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (35)
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| Relations |
| BioProject |
PRJNA340370 |
| SRA |
SRP083135 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE86148_CLIP-seq_gene_counts.csv.gz |
240.1 Kb |
(ftp)(http) |
CSV |
| GSE86148_gene_counts.csv.gz |
1.6 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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