GSM4063817: D07; Homo sapiens; RNA-Seq
For RNA extraction, 2–10 sections of 10 µm-thick formalin-fixed paraffin-embedded tissue were prepared. After macrodissection of the tumor area, RNA were extracted using the Recover All Total Nucleic Acid Isolation kit (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer's protocol. RNA concentrations were determined with the Qubit RNA HS Assay Kit and Qubit 3.0 Fluorometer (Thermo Fisher Scientific). RNA was reverse-transcribed into cDNA using the SuperScript VILO™ cDNA synthesis kit (Thermo Fisher Scientific). Libraries were prepared manually using the Ion AmpliSeq™ Library kit 2.0 (Life Technologies, Carlsbad, CA, USA) and Oncomine™ Immune Response Research Assay (Thermo Fisher Scientific). A 50-pM pool of RNA libraries was used for sequencing of a 395-gene panel focused on diverse immunological processes including tumor infiltration by immune cells, and other key immune functions. Template preparation and enrichment were performed using an Ion Chef™ system (Thermo Fisher Scientific) and Ion 520™ & Ion 530™ Kit – Chef (Thermo Fisher Scientific). Sequencing was performed on an Ion S5™ XL Sequencer using an Ion 530 Chip and Ion S5™ sequencing kit (all from Thermo Fisher Scientific).
GEO
GSM4063817
GEO Accession
GSM4063817