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RUNX2 as a novel Biomarker for early identification of Patients Progressing to Advanced-Stage Mycosis Fungoides

GSE275677 Homo sapiens (human) RNA-seq (gene expression) 68 samples Submitted 2024/09/13 Platform GPL34281
At a glance

RNA-seq (gene expression) · human · 68 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
68 samples
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
RUNX2 as a novel biomarker for early identification of patients progressing to advanced-stage mycosis fungoidesFrontiers in oncology · 2024
Summary (written by the submitters)
Here, we used spatial transcriptomics on skin samples at time-of-diagnosis to enable prediction of patients who later progressed to advanced stages of MF. Formalin-fixed, paraffin-embedded skin biopsies at time of diagnosis from six patients with MF who progressed to advanced stages of disease within 4 months to 12 years after diagnosis, and nine patients who remained in early-stage disease over 9 to 27 years were analyzed using the GeoMx Digital Spatial Profiler to capture spatially resolved high-plex RNA gene expression data.
Read the full summary ↓
Five different regions of interest (the epidermis, the basal layer of epidermis, CD4+ T-cells and neighboring cells, and Pautrier’s microabscesses) were profiled for further assessment.
Published in
RUNX2 as a novel biomarker for early identification of patients progressing to advanced-stage mycosis fungoides
Danielsen M, Emmanuel T, Nielsen MM et al. · Frontiers in oncology 2024 · PMID 39435287 · doi:10.3389/fonc.2024.1421443
This dataset
Open GSE275677 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 GSE275677_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 PRJNA1152558 and SRA study SRP528674. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39435287) ↗
Samples in this study

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