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Inflammatory pathways confer resistance to chemoradiotherapy in anal squamous cell carcinoma

GSE254331 Homo sapiens (human) RNA-seq (gene expression) 98 samples Submitted 2024/03/18 Platform GPL16791
At a glance

RNA-seq (gene expression) · human · 98 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)
Topic
Anal cancerThis series is part of our curated briefing on it.
Samples
98 samples: 78 × cCR.ASCC vs 20 × PD.ASCCGroups 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
Inflammatory pathways confer resistance to chemoradiotherapy in anal squamous cell carcinomaNPJ precision oncology · 2024
Summary (written by the submitters)
Acantholytic squamous cell carcinoma (ASCC) is associated with immunosuppression and infection with human papillomavirus (HPV). Response to standard chemoradiotherapy (CRT) varies considerably. A comprehensive molecular characterization of CRT resistance is lacking, and little is known about the interplay between tumor immune contexture, host immunity, and immunosuppressive and/or immune activating effects of CRT.
Read the full summary ↓
Patients with histologically confirmed, localized ASCC, treated between 1998 and 2019 at three different sites (Frankfurt, Berlin, Tübingen) of the German Cancer Consortium (DKTK) were included. All patients received 5-FU/MMC-based CRT. Patient cohorts for molecular analysis were defined based on availability and quality of samples, including baseline formalin fixed paraffin embedded biopsies for immunohistochemistry (n=130), baseline RNA sequencing (n=98), peripheral blood immune profiling by sequential multiparametric flow cytometry (n=47), and serum cytokine multiplex assays measurement (n=35). Tumor response, freedom from locoregional failure (FFLF), and freedom from distant metastasis (FFDM) were correlated with clinicopathologic and molecular findings.
Published in
Inflammatory pathways confer resistance to chemoradiotherapy in anal squamous cell carcinoma
Martin D, Rödel F, Hehlgans S et al. · NPJ precision oncology 2024 · PMID 38653773 · doi:10.1038/s41698-024-00585-y
This dataset
Open GSE254331 in finder → Find more human RNA-seq datasets → Anal cancer landscape →
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 GSE254331_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 PRJNA1069754 and SRA study SRP486182. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38653773) ↗
Study design
78 × cCR.ASCC vs 20 × PD.ASCC

Supports a between-group comparison across 98 samples.

How we read this: 2 replicated groups read from 98 sample titles; they account for 98 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

+ 58 more — browse all 98 samples with per-sample file links →

More Anal cancer datasets

Search all human RNA-seq datasets in GEO →

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.