GEO series

mRNA-seq analysis of S100A16-mediated alternative splicing in lung adenocarcinoma under oxidative stress

GSE330179 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2026/08/06 Platform GPL24676

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)
Topic: Lung cancerThis series is part of our curated briefing on it.
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.

Summary (written by the submitters)

Lung adenocarcinoma (LUAD) cells develop adaptive mechanisms to survive high oxidative stress in the tumor microenvironment. This study aims to elucidate the role of S100A16, a calcium-binding protein, in regulating mitochondrial quality control and oxidative stress resistance. We performed polyA-enriched mRNA sequencing on human lung adenocarcinoma A549 cells with stable knockdown of S100A16, hnRNPM (a splicing factor identified as S100A16 interactor) or MagoHB (a negative control interactor), with or without 100μM H₂O₂ treatment for 2 hours (3 biological replicates per group).

Read the full summary ↓

Transcriptomic analysis revealed that S100A16 translocates to the nucleus under oxidative stress and interacts with hnRNPM to modulate alternative splicing of mitochondrial genes (e.g., LETMD1), thereby maintaining mitochondrial morphology, membrane potential and respiratory function. These data provide mechanistic insights into S100A16 as a potential therapeutic target for LUAD.

This dataset

Open GSE330179 in finder → Find more human RNA-seq datasets → Lung cancer landscape →

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 GSE330179_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 PRJNA1463067 and SRA study SRP698231. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

6 conditions, mostly in triplicate

A549 wild type, untreated, ×3 A549 wild type, 100μM H₂O₂ 2h, ×3 A549 S100A16 knockdown, untreated, ×3 A549 S100A16 knockdown, 100μM H₂O₂ 2h, ×3 A549 hnRNPM knockdown, untreated, ×3 A549 MagoHB knockdown, untreated, ×3

Supports a case/control comparison: 3 samples read as cases, 3 as controls.

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

GSM9720506 A549 wild type, untreated, replicate 1 A549 wild type, untreat…
GSM9720507 A549 wild type, untreated, replicate 2 A549 wild type, untreat…
GSM9720508 A549 wild type, untreated, replicate 3 A549 wild type, untreat…
GSM9720509 A549 wild type, 100μM H₂O₂ 2h, replicate 1 A549 wild type, 100μM H…
GSM9720510 A549 wild type, 100μM H₂O₂ 2h, replicate 2 A549 wild type, 100μM H…
GSM9720511 A549 wild type, 100μM H₂O₂ 2h, replicate 3 A549 wild type, 100μM H…
GSM9720512 A549 S100A16 knockdown, untreated, replicate 1 A549 S100A16 knockdown,…
GSM9720513 A549 S100A16 knockdown, untreated, replicate 2 A549 S100A16 knockdown,…
GSM9720514 A549 S100A16 knockdown, untreated, replicate 3 A549 S100A16 knockdown,…
GSM9720515 A549 S100A16 knockdown, 100μM H₂O₂ 2h, replicate 1 A549 S100A16 knockdown,…
GSM9720516 A549 S100A16 knockdown, 100μM H₂O₂ 2h, replicate 2 A549 S100A16 knockdown,…
GSM9720517 A549 S100A16 knockdown, 100μM H₂O₂ 2h, replicate 3 A549 S100A16 knockdown,…
GSM9720518 A549 hnRNPM knockdown, untreated, replicate 1 A549 hnRNPM knockdown, …
GSM9720519 A549 hnRNPM knockdown, untreated, replicate 2 A549 hnRNPM knockdown, …
GSM9720520 A549 hnRNPM knockdown, untreated, replicate 3 A549 hnRNPM knockdown, …
GSM9720521 A549 MagoHB knockdown, untreated, replicate 1 A549 MagoHB knockdown, …
GSM9720522 A549 MagoHB knockdown, untreated, replicate 2 A549 MagoHB knockdown, …
GSM9720523 A549 MagoHB knockdown, untreated, replicate 3 A549 MagoHB knockdown, …

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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.