RNA Extraction and Sequencing from PDX Tumors

For RNA extraction, PDX tumor tissues were processed and homogenized in 300 mL of QIAzol as described earlier (12 (link)). Illumina TruSeq RNA Sample Preparation v2 Guide was used to construct libraries from 1 μg total RNA. The cDNA library was validated on the Agilent 2100 Bioanalyzer DNA-1000 chip. Sequencing was performed as described previously (12 (link)). The bioinformatics strategy outlined in the Keysar and colleagues was used (12 (link)).

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Bhatia S., Sharma J., Bukkapatnam S., Oweida A., Lennon S., Phan A., Milner D., Uyanga N., Jimeno A., Raben D., Somerset H., Heasley L, & Karam S.D. (2018). Inhibition of EphB4–Ephrin-B2 Signaling Enhances Response to Cetuximab-Radiation Therapy in Head and Neck Cancers. Clinical cancer research : an official journal of the American Association for Cancer Research, 24(18), 4539-4550.

Publication 2018

TruSeq RNA Sample Preparation v2 Guide Agilent 2100 Bioanalyzer DNA-1000 chip

Cdna library Dna chip Tissues Tumor

Corresponding Organization : University of Colorado Denver

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Variable analysis

independent variables

RNA extraction protocol
Library construction method (Illumina TruSeq RNA Sample Preparation v2 Guide)
Sequencing method (as described previously)

dependent variables

Gene expression profile from RNA sequencing

control variables

PDX tumor tissues
Total RNA input (1 μg)
Bioinformatics strategy (as outlined in Keysar and colleagues)

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