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PCR analyses

MD Martin G. Dalin
NK Nora Katabi
MP Marta Persson
KL Ken-Wing Lee
VM Vladimir Makarov
AD Alexis Desrichard
LW Logan A. Walsh
LW Lyndsay West
ZN Zaineb Nadeem
DR Deepa Ramaswami
JH Jonathan J. Havel
FK Fengshen Kuo
KC Kalyani Chadalavada
GN Gouri J. Nanjangud
IG Ian Ganly
NR Nadeem Riaz
AH Alan L. Ho
CA Cristina R. Antonescu
RG Ronald Ghossein
GS Göran Stenman
TC Timothy A. Chan
LM Luc G. T. Morris
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cDNA was synthesized from tumor RNA using Superscript III Reverse Transcriptase (Thermo Fisher Scientific). For validation of fusion genes detected by RNA-seq, cDNA was amplified by reverse transcriptase PCR (RT-PCR) using a Master Cycler Pro (Eppendorf, Hamburg, Germany) and visualized on a 1.5% agarose gel. See Supplementary Fig. 35 for full pictures of gels that were cropped in main figures. For gene expression analysis, cDNA was analyzed by quantitative PCR using a QuantStudio 6 Flex (Applied Biosystems, Waltham, MA, USA). The ΔΔCt values were calculated with the 2−(ΔΔCt) method. The analyzed genes were normalized to the reference genes STLM (for cell culture experiments) or GAPDH (for analysis of tumor tissue). All primer sequences are listed in Supplementary Table 8.

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