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Bulk RNA-seq sample preparation

VP Vanda Póvoa
CA Cátia Rebelo de Almeida
MM Mariana Maia-Gil
DS Daniel Sobral
MD Micaela Domingues
MM Mayra Martinez-Lopez
MF Miguel de Almeida Fuzeta
CS Carlos Silva
AG Ana Rita Grosso
RF Rita Fior
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SW480 and SW620 tumors were dissected from zebrafish xenografts at 2 dpi. A pool of ~30 tumors from each type of tumor and independent experiments was collected in RNAlater solution (#AM7020, Ambion) and kept at −20 °C until RNA extraction. The engraftment rate (determined at 4 dpi with remaining zebrafish xenografts) of SW480 and SW620 used for gene expression analysis was the following: SW480_B—8%, SW480_A—30%, and SW480_7—31.5%; SW620_1—92.4%, SW620_2—92%, SW620_5—97.2%, and SW620_7—98.3%. To study the genetic signatures of the underlying observed phenotypes (regressors and progressors), total RNA was extracted from the dissected tumors using Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) and further purified with RNeasy Plus Micro Kit (Qiagen), in accordance with the manufacturer’s instructions.

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