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The zebrafish heart harbors a thermogenic beige fat depot analog of human epicardial adipose tissue

GSE227670 Danio rerio (zebrafish) RNA-seq (gene expression) 18 samples Submitted 2024/03/19 Platform GPL24995Platform GPL30172
At a glance

RNA-seq (gene expression) · zebrafish · 18 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
Danio rerio (zebrafish)
Samples
18 samples: 6 conditions, mostly in triplicateGroups 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
The zebrafish heart harbors a thermogenic beige fat depot analog of human epicardial adipose tissueCell reports · 2024
Summary (written by the submitters)
The main goal of this study was to examine the presence and specific transcriptomic profile of epicardial adipose tissue (eAT) in zebrafish. We assessed how cold treatment affects the epicardial adipose tissue. Additional we provided some key differences between human, mouse and zebrafish epicardial adipose tissue.
Published in
The zebrafish heart harbors a thermogenic beige fat depot analog of human epicardial adipose tissue
Morocho-Jaramillo PA, Kotlar-Goldaper I, Zakarauskas-Seth BI et al. · Cell reports 2024 · PMID 38507414 · doi:10.1016/j.celrep.2024.113955
This dataset
Open GSE227670 in finder → Find more 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 GSE227670_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 PRJNA946307 and SRA study SRP428087. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38507414) ↗
Study design
6 conditions, mostly in triplicate
eAT, epicardial fat ×3 vAT, visceral fat ×3 control eAT, epicardial fat ×3 cold eAT, epicardial fat ×3 young mouse eAT, epicardial fat ×3 aged mouse eAT, epicardial fat ×3

Supports a between-group comparison across 18 samples.

How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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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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.