Precision RNAi using synthetic shRNAmir target sites
- Research Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University at Vienna and Medical University of Vienna, Vienna BioCenter (VBC), Austria
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse, Austria
- Medical University of Vienna, Vienna BioCenter, Austria
Figures
Figure 1 with 1 supplement
Design and selection ARTi-shRNAmirs.
(A) Schematic outline of the ARTi approach. (B) Sequence logo (https://weblogo.berkeley.edu) displaying nucleotide position biases of 2161 shRNAs with exceptionally high Designer of Small …
Figure 1—figure supplement 1
Design and selection ARTi-shRNAmirs.
(A) Sequence logo displaying nucleotide position biases of seed sequences (guide positions 2–8) with the lowest off-target score in siSPOTR analysis (top 1%). (B) Sequence logo displaying position …
Figure 2 with 3 supplements
Experimental validation of the artificial RNA interference (ARTi) approach.
(A) Schematic of EGFRdel19::V5::dsRed::ARTi engineering in PC-9 cells. Blue color denotes overexpressed ARTi variant. Green denotes endogenous gene. (B) Western blot demonstrating knockdown of EGFRde…
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Figure 2—source data 1
Original blots for Figure 2B and Figure 2—figure supplement 1B.
- https://cdn.elifesciences.org/articles/84792/elife-84792-fig2-data1-v1.zip
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Figure 2—source data 2
Original blots for Figure 2F.
- https://cdn.elifesciences.org/articles/84792/elife-84792-fig2-data2-v1.zip
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Figure 2—source data 3
Original blots for Figure 2J.
- https://cdn.elifesciences.org/articles/84792/elife-84792-fig2-data3-v1.zip
Figure 2—figure supplement 1
Validation of artificial RNA interference (ARTi) in vitro and in vivo – EGFR.
(A) Functional validation of the EGFRdel19 construct in Ba/F3 cells. Provided are GI50 values (nM) for indicated conditions and compounds (parental cells IL-3-dependent; other cells dependent on …
Figure 2—figure supplement 2
Validation of artificial RNA interference (ARTi) in vitro and in vivo – KRAS.
(A) Schematic of MIA PaCa-2 genome engineering. (B) AMG-510 GI50 values in MIA PaCa-2 parental and engineered cells. Numbers represent GI50 value calculated from three technical repeats. Three …
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Figure 2—figure supplement 2—source data 1
Original blots for Figure 2—figure supplement 2D.
- https://cdn.elifesciences.org/articles/84792/elife-84792-fig2-figsupp2-data1-v1.zip
Figure 2—figure supplement 3
Validation of artificial RNA interference (ARTi) in vitro and in vivo – STAG1.
(A) Schematic of synthetic lethal interaction between STAG1 and STAG2. Cells survive loss of either paralog but are incapable of growing upon combined loss of STAG1 and STAG2. (B) Western blot …
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Figure 2—figure supplement 3—source data 1
Original blots for Figure 2—figure supplement 3B.
- https://cdn.elifesciences.org/articles/84792/elife-84792-fig2-figsupp3-data1-v1.zip
