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NICO Myriad system Improves sample quality for molecular pathology assays

GSE298049 Homo sapiens (human) RNA-seq (gene expression) 29 samples Submitted 2026/06/30 Platform GPL18460
At a glance

RNA-seq (gene expression) · human · 29 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Samples
29 samples: 16 × ST-FF vs 13 × NICO-FFGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
NICO Myriad Automated Preservation System improves meningioma sample quality for molecular pathology assaysJournal of neuropathology and experimental neurology · 2026
Summary (written by the submitters)
Meningiomas are commonly treated through surgery, radiation, or chemotherapy, based. These decisions are guided by pathological interpretation which traditionally uses the WHO classification schema. Current diagnostic methods based on FFPE samples often fall short of providing precise treatment, and hence multiple revisions have been generated such as cImpact8.
Read the full summary ↓
However, emerging molecular techniques, such as circular RNA (circRNA) profiling show potential to enhance diagnostic accuracy but are limited by degradation caused by FFPE process. To overcome this challenge, we tested the extent to which the NICO Myriad system enhances tissue preservation. The NICO Myriad system extracts fresh tissue in situ using a refrigerated chamber and Ringer’s Lactate fluid. This study aims to compare the efficiency of Traditional and NICO tissue extraction protocols for meningioma resection, focusing on circRNA profiles as clinical biomarkers. We performed circRNA sequencing in 20 patients, collected under identical tumor resection conditions. We performed T-test to compare RNA extraction and sequencing quality, circRNA detection and profile between protocols. DEseq analysis was applied to circRNAs Differential Expression, and Weighted Gene Co-expression Network Analysis (WGCNA) correlated with clinical features followed by GO enrichment. NICO protocol enhances RNA integrity (p=0.0023), yielding a high-quality data (>Q30 median=95%) which reduced variation of circRNA detection. WGCNA identified two modules differentiating the protocols, while two modules were related with WHO Grade 2 associated with cellular metabolism, and epitranscriptomic regulation. We conclude that the NICO protocol, which offers a homeostatic environment, significantly improves the precision of circRNA detection.
Published in
NICO Myriad Automated Preservation System improves meningioma sample quality for molecular pathology assays
de Mendonça Fernandes GM, Wu KC, Palmer J et al. · Journal of neuropathology and experimental neurology 2026 · PMID 42475233 · doi:10.1093/jnen/nlag030
This dataset
Open GSE298049 in finder → Find more human RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE298049_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1267168 and SRA study SRP588016. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42475233) ↗
Study design
16 × ST-FF vs 13 × NICO-FF

Supports a between-group comparison across 29 samples.

How we read this: 2 replicated groups read from 29 sample titles; they account for 29 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study
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