GSE106804 ( lncRNA+mRNA )

glioblastoma ( glioma )

Engineered Nanointerfaces for Microfluidic Isolation and Molecular Profiling of Tumor-specific Extracellular Vesicles

Cancer : 8 / Control : 6

The paired-end reads from the three sequencing runs were combined and aligned to the hg38 genome from http://genome.ucsc.edu using the STAR v2.4.0h aligner with default settings. Reads that did not map or mapped to multiple locations were discarded. Duplicate reads were marked using the MarkDuplicates tool in picard-tools-1.8.4 and were removed.

Tumor-EVs were captured on a nanostructured interface through immunoaffinity immobilization in a microfluidic channel containing herringbone (HB) structure for efficient mixing (EVHB-Chip). Processing serum and plasma samples from glioblastoma multiforme (GBM) patients, isolated tumor EVs were analyzed using next-generation RNA sequencing analysis, and identified genes specific to glioblastoma as well as transcripts that are hallmarks for the four genetic subtypes of disease (e.g., classical, mesenchymal, neural, and pro-neural).

Plasma or serum isolated from 13 GBM patients than run through the EVHB-Chip coated with antibodies.(EGFR, EGFRvIII, PDGFR) Isolated Evs analysed using next-generation RNA sequencing analysis.

Reátegui E, van der Vos KE, Lai CP, Zeinali M et al. Engineered nanointerfaces for microfluidic isolation and molecular profiling of tumor-specific extracellular vesicles. Nat Commun 2018 Jan 12;9(1):175. PMID: 29330365

Qiazol-Chloroform extraction performed, and RNA purified by miRNeasy mini kit according to the manufacturers protocol. (Qiagen, Valencia, MA)

total RNA

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