Non-coding RNA profiling by high throughput sequencing
Summary
Using a pooled shRNA library, we performed a focused screen of 81 shRNAs selected for involvement in response to chemotherapy in an ex vivo 3D primary tumor cell culture system. Our results establish Ankrd35, a previously uncharacterized ankyrin repeat domain protein, as an important mediator of chemoresistance in vivo.
Overall design
We analyze shRNA abundance at two different timepoints using 4 biological replicates for genes predicted to play a functional role in chemoresistance and re-growth of the tumor after chemotherapy and compare these results to LKR10 cells (a similar murine NSCLC cell line grown in 2D culture) treated in parallel with cisplatin. The first analysis compares untreated groups T1 v. T0 for any in vivo shRNA vulnerabilities in mouse-derived xenografts (MDXs) and LKR10 cells; the second analysis compares cisplatin treated T1 v. untreated T1 groups for chemosensitizers in MDXs and LKR10 cells..
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