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Effect of TOP2B deletion or catalytic inhibition on gene expression in iPSC-derived human cardiomyocytes

GSE262148 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2025/07/24 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 24 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
24 samples: 6 conditions, mostly with about 4 replicates eachGroups 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)
DNA topoisomerase IIB (TOP2B) is required for the correct execution of certain developmental transcription programs. Here, we have compared the transcriptional changes accompanying differentiation of wild type and TOP2B null human iPSC cells to beating cardiomyocytes. In addition we assess the transcriptional effect of short term (3hr) application of two TOP2B catalytic inhibitors in iPSC-derived cardiomyocytes.
This dataset
Open GSE262148 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 GSE262148_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 PRJNA1090474 and SRA study SRP497010. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
6 conditions, mostly with about 4 replicates each
WT iPSC-derived cardiomyocytes, untreated, bi… ×4 WT iPSC-derived cardiomyocytes, Dexrazoxane, … ×4 TOP2B null iPSC-derived cardiomyocytes, untre… ×4 WT iPSC-derived cardiomyocytes, JM-437, biol ×4 WT undifferentiated iPSC cells, biol ×4 TOP2B null undifferentiated iPSC cells, biol ×4

Supports a between-group comparison across 24 samples.

How we read this: 6 replicated groups read from 24 sample titles; they account for 24 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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