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| Status |
Public on Oct 25, 2016 |
| Title |
Pan-cancer transcriptomic analysis associates long non-coding RNAs with key mutational driver events |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
To identify genes regulated by NFE2L2 (Nrf2), we selected a lung cancer cell line (A549) in which NFE2L2 is normally active. Three transfections using siRNAs targeting NFE2L2 and four control transfections using two different negative control siRNAs were done. As a result, we found several genes up or down regulated in response to NFE2L2 inactivation in these cells.
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| Overall design |
A549 cells were cultured, and 250,000 cells were transfected with Lipofectamine RNAiMAX reagent containing 5 nmol siRNA particles in a 6-well plate. Three transfections with siRNAs targeting NFE2L2 were performed, using three independent duplexes, while four control transfections were done using two different control duplexes, in addition to one mock (Lipofectamine only) transfection. RNA was prepared using the RNeasy Mini kit. 8 strand-specific total RNA-seq libraries were generated on an Illumina NextSeq 500. Between 50.5 and 60.6 million reads were obtained per sample. Reads were aligned to hg19 genome, at an alignment rate exceeding 94.4% for all samples.
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| Contributor(s) |
Ashouri A, Sayin VI, Van den Eynden J, Singh SX, Papagiannakopoulos T, Larsson E |
| Citation |
Ashouri, A. et al. Pan-cancer transcriptomic analysis associates long non-coding RNAs with key mutational driver events. Nat. Commun. 7, 13197
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| BioProject |
PRJNA299393 |
| Submission date |
Nov 27, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Arghavan Ashouri |
| E-mail(s) |
arghavan.ashouri@gu.se
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| Organization name |
University of Gothenburg
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| Department |
Medical Biochemistry and Cell Biology
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| Street address |
Medicinaregatan 9A
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| City |
Gothenburg |
| ZIP/Postal code |
41390 |
| Country |
Sweden |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (8)
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| Relations |
| SRA |
SRP066737 |
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