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Cytotoxic T-cells drive out come in Inflammatory Dilated Cardiomyopathy

GSE278521 Homo sapiens (human) RNA-seq (gene expression) 37 samples Submitted 2024/12/31 Platform GPL21697
At a glance

RNA-seq (gene expression) · human · 37 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
37 samples: 27 × Inflammatory dilated cardiomyopathy vs 10 × Non-inflammatory dilated cardiomyopathyGroups 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.
Summary (written by the submitters)
Dilated cardiomyopathy (DCM) is often driven by myocarditis, however, the underlying immune mechanism remains unknown. We performed bulk-RNA sequencing of endomyocardial biopsies taken 9 months (interquartile range 4-26 months) from DCM diagnosis and we found that in patients with high cardiac inflammation (at least 7 CD3+ T-cells per mm2 or at least 14 CD45+ leukocyte per mm2 endomyocardial biopsy) Perforin-1, Granzyme-A, Granzyme-H, and Interleukin-17 receptor subunit C
Read the full summary ↓
were more often expressed compared to patients with low cardiac inflammation (less than 3 CD3+ T-cells per mm2 and less than 5 CD45+ leukocytes per mm2 endomyocardial biopsy).
This dataset
Open GSE278521 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 GSE278521_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 PRJNA1167699 and SRA study SRP535954. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
27 × Inflammatory dilated cardiomyopathy vs 10 × Non-inflammatory dilated cardiomyopathy

Supports a between-group comparison across 37 samples.

How we read this: 2 replicated groups read from 37 sample titles; they account for 37 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
Datasets on a similar topic

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