Bulk RNA Sequencing of Melanoma Tumors

Bulk RNA sequencing was performed on melanoma tumors, as previously described^{37 (link),38 (link)}. In brief, RNA was extracted from tumors using the RNeasy PowerLyzer Tissue & Cells Kit (QIAGEN) and quality was assessed with a 2100 Bioanalyzer System (Agilent Technologies). Ribosomal RNA was depleted Kapa RNA HyperPrep Kit with RiboErase (Kapa Biosystems, Inc., Cape Town, South Africa). Sequencing libraries were generated using TruSeq RNA sample prep kits (Illumina) and sequenced on an Illumina HiSeq 2500 using 2 × 150 bp paired-end reads with a target of 20–25 million reads per sample. Raw sequencing files were aligned to the GRCh38 human genome.

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Hafler D., Lu B., Lucca L., Lewis W., Wang J., Nogeuira C., Heer S., Axisa P.P., Buitrago-Pocasangre N., Pham G., Kojima M., Wei W., Aizenbud L., Bacchiocchi A., Zhang L., Walewski J., Chiang V., Olino K., Clune J., Halaban R., Kluger Y., Coyle A., Kisielow J., Obermair F.J, & Kluger H. (2024). Circulating Tumor Reactive KIR+CD8+ T cells Suppress Anti-Tumor Immunity in Patients with Melanoma. Research Square.

Publication Preprint 2024

RNeasy PowerLyzer Tissue & Cells Kit 2100 Bioanalyzer System Kapa RNA HyperPrep Kit with RiboErase TruSeq RNA sample prep kits HiSeq 2500

Corresponding Organization :

Other organizations : Yale University, AC Immune (Switzerland)

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Ribosomal RNA was depleted using the Kapa RNA HyperPrep Kit with RiboErase (Kapa Biosystems, Inc., Cape Town, South Africa)
Sequencing libraries were generated using TruSeq RNA sample prep kits (Illumina)
Sequencing was performed on an Illumina HiSeq 2500 using 2 × 150 bp paired-end reads with a target of 20–25 million reads per sample

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