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Knockdown of RNA editing proteins reshapes the HepaRG transcriptome and pharmacogene expression

GSE309947 Homo sapiens (human) RNA-seq (gene expression) 19 samples Submitted 2026/03/02 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 19 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
19 samples: 7 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
Knockdown of RNA editing proteins reshapes the HepaRG transcriptome and pharmacogene expressionScientific reports · 2026
Summary (written by the submitters)
The RNA-editing proteins, ADAR and ADARB1, regulate gene expression through editing-dependent and editing-independent mechanisms. Both proteins have been shown to have essential functions in the liver, including regulating the expression of drug-metabolizing enzymes. Here, using RNA-Seq, we profiled widespread changes to the hepatic transcriptome after knockdown (KD) of either ADAR or ADARB1 in HepaRG cells.
Read the full summary ↓
Nearly a thousand pharmacogenes had altered expression or alternative splicing across both KDs, with splice isoform switches occurring for both HNF4A and CYP2C9. The two ADAR proteins largely affected different sets of genes, with KD of ADAR having more widespread effects than KD of ADARB1. Subsequent analyses of differential editing indicated that most transcriptomic alterations were independent of RNA editing. As KD of ADAR stimulates a type I interferon response; we compared changes to gene expression between siADAR and IFNα treatment. While both conditions triggered interferon signaling, their transcriptional fingerprints differed substantially; nevertheless, 70% of the genes dysregulated by ADAR KD were restored by BX795, an inhibitor of the type I response, supporting that many of the effects of siADAR were related to the induction of an immune pathway. Overall, our results suggest that the ADARs play key roles in maintaining liver homeostasis and the expression of many pharmacogenes, especially those involved in drug metabolism and disposition.
Published in
Knockdown of RNA editing proteins reshapes the HepaRG transcriptome and pharmacogene expression
Collins JM, Yu F, Zhang Y et al. · Scientific reports 2026 · PMID 41813840 · doi:10.1038/s41598-026-43323-z
This dataset
Open GSE309947 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 GSE309947_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 PRJNA1364030 and SRA study SRP644571. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41813840) ↗
Study design
7 conditions, mostly in triplicate
HepaRG cells, siNC Control, ×3 HepaRG cells, siADAR, ×3 HepaRG cells, siADARB1, ×3 HepaRG cells, siNC Control for BX795&IFNa tre… ×3 HepaRG cells, BX795, ×3 HepaRG cells, IFNa, ×2 HepaRG cells, BX795 & siADAR, ×2

Supports a between-group comparison across 19 samples.

How we read this: 7 replicated groups read from 19 sample titles; they account for 19 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
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