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| Status |
Public on Jul 04, 2023 |
| Title |
Precision RNAi using synthetic shRNAmir target sites |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Loss-of-function genetic tools are widely applied for validating therapeutic targets, but their utility remains limited by incomplete on- and uncontrolled off-target effects. We describe artificial RNA interference (ARTi) based on synthetic, ultra-potent, off-target-free shRNAs that enable efficient, inducible, and reversible suppression of any gene upon introduction of a synthetic target sequence into non-coding transcript regions. ARTi establishes a scalable loss-of-function tool with full control over on- and off-target effects.
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| Overall design |
Quant-seq of RKO and HT-1080 human cell lines transduced with ARTi.6570, ARTi.6634, ARTi.6786 artificial short-hairpin RNA constructs or with empty vector control (+/- trametinib treatment) in biological triplicates.
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| Contributor(s) |
Hoffman T, Hörmann A, Corcokovic M, Zmaikovic J, Hinterndorfer M, Salkanovic J, Spritzer F, Köferle A, Gitschtaler K, Popa A, Oberndorfer S, Andersch F, Feller M, Ruppert J, Chetta P, Wurm M, Zuber J, Neumüller RA |
| Citation(s) |
37552050, 38536927 |
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| Submission date |
Nov 21, 2022 |
| Last update date |
Apr 04, 2024 |
| Contact name |
Florian Andersch |
| E-mail(s) |
florian.andersch@imp.ac.at
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| Organization name |
Institute of Molecular Pathology
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| Lab |
Johannes Zuber
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| Street address |
Campus-Vienna-Biocenter 1
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| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (36)
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| GSM6744303 |
RKO cell line, ARTi.6634 shRNA, rep1 |
| GSM6744304 |
RKO cell line, ARTi.6634 shRNA, rep2 |
| GSM6744305 |
RKO cell line, ARTi.6634 shRNA, rep3 |
| GSM6744306 |
RKO cell line, ARTi.6786 shRNA, rep1 |
| GSM6744307 |
RKO cell line, ARTi.6786 shRNA, rep2 |
| GSM6744308 |
RKO cell line, ARTi.6786 shRNA, rep3 |
| GSM6744309 |
RKO cell line, REN.713 shRNA, rep1 |
| GSM6744310 |
RKO cell line, REN.713 shRNA, rep2 |
| GSM6744311 |
RKO cell line, REN.713 shRNA, rep3 |
| GSM6744312 |
RKO cell line, empty vector, rep1 |
| GSM6744313 |
RKO cell line, empty vector, rep2 |
| GSM6744314 |
RKO cell line, empty vector, rep3 |
| GSM6744315 |
RKO cell line, empty vector, 130nM trametinib treatment for 24 hrs, rep1 |
| GSM6744316 |
RKO cell line, empty vector, 130nM trametinib treatment for 24 hrs, rep2 |
| GSM6744317 |
RKO cell line, empty vector, 130nM trametinib treatment for 24 hrs, rep3 |
| GSM6744318 |
HT1080 cell line, ARTi.6570 shRNA, rep1 |
| GSM6744319 |
HT1080 cell line, ARTi.6570 shRNA, rep2 |
| GSM6744320 |
HT1080 cell line, ARTi.6570 shRNA, rep3 |
| GSM6744321 |
HT1080 cell line, ARTi.6634 shRNA, rep1 |
| GSM6744322 |
HT1080 cell line, ARTi.6634 shRNA, rep2 |
| GSM6744323 |
HT1080 cell line, ARTi.6634 shRNA, rep3 |
| GSM6744324 |
HT1080 cell line, ARTi.6786 shRNA, rep1 |
| GSM6744325 |
HT1080 cell line, ARTi.6786 shRNA, rep2 |
| GSM6744326 |
HT1080 cell line, ARTi.6786 shRNA, rep3 |
| GSM6744327 |
HT1080 cell line, REN.713 shRNA, rep1 |
| GSM6744328 |
HT1080 cell line, REN.713 shRNA, rep2 |
| GSM6744329 |
HT1080 cell line, REN.713 shRNA, rep3 |
| GSM6744330 |
HT1080 cell line, empty vector, rep1 |
| GSM6744331 |
HT1080 cell line, empty vector, rep2 |
| GSM6744332 |
HT1080 cell line, empty vector, rep3 |
| GSM6744333 |
HT1080 cell line, empty vector, 960nM trametinib treatment for 24 hrs, rep1 |
| GSM6744334 |
HT1080 cell line, empty vector, 960nM trametinib treatment for 24 hrs, rep2 |
| GSM6744335 |
HT1080 cell line, empty vector, 960nM trametinib treatment for 24 hrs, rep3 |
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| Relations |
| BioProject |
PRJNA903783 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE218404_HT1080_normalized_counts.tsv.gz |
808.5 Kb |
(ftp)(http) |
TSV |
| GSE218404_RKO_normalized_counts.tsv.gz |
755.1 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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