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Differential RNA-seq analysis of MB135iDUX4 with siRNA mediated knockdown of KLF17 and KLF18

GSE316237 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2026/06/10 Platform GPL34281
At a glance

RNA-seq (gene expression) · human · 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
Homo sapiens (human)
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
KLF18 is a necessary component of the DUX4-initiated transcriptional network and a candidate locus for phenotypic diversityGenes & development · 2026
Summary (written by the submitters)
DUX4 initiates the first wave of zygotic genome activation (ZGA) in the human embryo and its misexpression in skeletal muscle causes facioscapulohumeral muscular dystrophy (FSHD). However, other factors that help regulate ZGA-like transcription in human development and disease are still not fully understood. Here we identify Krüppel-like factor 18 (KLF18) as a component of a DUX4 feed-forward network that is necessary for expression of KLF17 and a subset of the DUX4-regulated totipotency-associated genes.
Read the full summary ↓
We mapped the genome-wide binding profile of KLF18 downstream of DUX4 and showed that its activity is influenced by DUX4 and chromatin accessibility. We find that in contrast to the rodent ortholog, human KLF18 has a predicted beta-solenoid structure composed of a variable number of tandem repeats (VNTRs) with multiple different structural variants in the human population. Expression of different KLF18 variants in combination with DUX4 showed similar transcriptional activity, whereas assessment of KLF18 structural variants in individuals with FSHD1 showed inconsistent association with disease severity that requires further study as a modifier locus. Together these findings establish the polymorphic transcription factor KLF18 as a critical component of a DUX4-initiated feed-forward network and a candidate locus for human diversity.
Published in
KLF18 is a necessary component of the DUX4-initiated transcriptional network and a candidate locus for phenotypic diversity
Hamm DC, O'Donnell AB, Bennett SR et al. · Genes & development 2026 · PMID 41986233 · doi:10.1101/gad.353253.125
This dataset
Open GSE316237 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 GSE316237_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 PRJNA1401840 and SRA study SRP661608. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41986233) ↗
Study design
6 conditions, mostly in triplicate
MB135_iDUX4ca_siCTRL_noDOX ×3 MB135_iDUX4ca_siCTRL_20hDOX ×3 MB135_iDUX4ca_siKLF17_noDOX ×3 MB135_iDUX4ca_siKLF17_20hDOX ×3 MB135_iDUX4ca_siKLF18_noDOX ×3 MB135_iDUX4ca_siKLF18_20hDOX ×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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