RNA-Seq Analysis of Tumor Tissues

Tumor tissues were frozen in RNAlater solution (Thermo #PA5-39542) and RNA was extracted using the RNeasy plus mini kit (Qiagen #74134). cDNA libraries were built using NEB Next Ultra RNA Library Prep Kit for Illumina (NEB #E7530S). Samples were multiplexed using NEB Next Multiplex Oligos for Illumina (NEB #E7710L). Samples were sequenced on an Illumina NexSeq 500 and reads were aligned to the mouse genome (GRCm38) using HiSat2^{58 (link)}. Mapped reads were counted using the featureCounts function from the Subread^{59 (link)} package. Differential expression between groups was calculated using edgeR^{50 (link)}.

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Patel R.S., Romero R., Watson E.V., Liang A.C., Burger M., Westcott P.M., Mercer K.L., Bronson R.T., Wooten E.C., Bhutkar A., Jacks T, & Elledge S.J. (2022). A GATA4-regulated secretory program suppresses tumors through recruitment of cytotoxic CD8 T cells. Nature Communications, 13, 256.

Publication 2022

RNAlater solution RNeasy plus mini kit NexSeq 500

Frozen Genome Library Mouse Oligos Tissues Tumor

Corresponding Organization :

Other organizations : Brigham and Women's Hospital, Massachusetts Institute of Technology, Harvard University, Howard Hughes Medical Institute

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Variable analysis

independent variables

Tissue type (tumor vs. not specified)

dependent variables

Gene expression levels

control variables

Mouse genome (GRCm38)

controls

None specified

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