NanoString PanCancer Pathways Panel Analysis

Samples were processed for analysis on the NanoString nCounter Flex system using the 770 gene nCounter^® PanCancer Pathways Panel (NanoString Technologies, Inc., Seattle, WA, USA), as previously reported (17 (link)). This panel assesses 13 cancer-associated canonical pathways related to basic cancer biology (Notch, Wnt, Hedgehog, Chromatin modification, Transcriptional regulation, DNA damage control, TGF-β, MAPK, STAT, PI3K, RAS, Cell cycle, Apoptosis). Briefly, 100 ng of total RNA, quantified by a Qubit Fluorometric System (Thermo Fisher Scientific, USA), from each sample was hybridized for 21 hours at 65°C, followed by purification and RNA/probe complex immobilization in nCounter PrepStation (NanoString Technologies, Inc., Seattle, WA, USA) and cartridge scanning in a digital analyzer (NanoString Technologies, Inc., Seattle, WA, USA), according to the manufacturer’s protocol. Reading with 280 field-of-views (FOVs) was used in the study samples.

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de Andrade D.A., da Silva L.S., Laus A.C., de Lima M.A., Berardinelli G.N., da Silva V.D., Matsushita G.D., Bonatelli M., da Silva A.L., Evangelista A.F., Carvalho J.P., Reis R.M, & dos Reis R. (2021). A 4-Gene Signature Associated With Recurrence in Low- and Intermediate-Risk Endometrial Cancer. Frontiers in Oncology, 11, 729219.

Publication 2021

NanoString nCounter Flex system Qubit Fluorometric System nCounter PrepStation digital analyzer

Apoptosis Cancer Cell cycle Chromatin Dna damage Fluorometric Gene Hedgehog Immobilization Pi3k Rna probe Tgf β Transcriptional

Corresponding Organization : Hospital de Câncer de Barretos

Other organizations : Instituto do Câncer do Estado de São Paulo, Universidade de São Paulo, University of Minho

Top 5 similar protocols

Variable analysis

independent variables

Gene panel (770 gene nCounter PanCancer Pathways Panel)

dependent variables

Gene expression levels of 13 cancer-associated canonical pathways

control variables

Amount of total RNA (100 ng) used for hybridization
Hybridization time (21 hours)
Hybridization temperature (65°C)
Number of field-of-views (FOVs) used for reading (280)

controls

No positive or negative controls were explicitly mentioned in the protocol.

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