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Changes to the global transcriptome in human U2OS and BJ cell lines as a result of STING activation

GSE254174 Homo sapiens (human) RNA-seq (gene expression) 48 samples Submitted 2024/09/19 Platform GPL30173Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 48 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
48 samples: 16 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
A TBK1-independent primordial function of STING in lysosomal biogenesisMolecular cell · 2024
Summary (written by the submitters)
Activation of Stimulator of interferon genes (STING) is well known to upregulate inflammation through canonical TBK1 signaling. STING is recently found to activate noncanonical functions through its transmembrane proton channel. Whether STING stimulates any transcription programs through its channel is unknown. In this study, we identified the transcription factor EB (TFEB) as a downstream effector of the STING channel.
Read the full summary ↓
TFEB is a transcriptional regulator of lysosomal biogenesis and autophagy. Using RNA sequencing approaches, we confirmed that STING activated transcriptional upregulation of lysosomal biogenesis and autophagy independently of TBK1.
Published in
A TBK1-independent primordial function of STING in lysosomal biogenesis
Lv B, Dion WA, Yang H et al. · Molecular cell 2024 · PMID 39423796 · doi:10.1016/j.molcel.2024.08.026
This dataset
Open GSE254174 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 GSE254174_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 PRJNA1068686 and SRA study SRP485786. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39423796) ↗
Study design
16 conditions, mostly in triplicate
U2OS MmSting350 minus DMXAA 8 hours b ×3 U2OS MmSting350 plus DMXAA 8 hours b ×3 BJ minus cGAMP 6 hours b ×3 BJ plus cGAMP 6 hours b ×3 BJ STING KO minus cGAMP 6 hours b ×3 BJ STING KO plus cGAMP 6 hours b ×3 BJ minus cGAMP 12 hours b ×3 BJ plus cGAMP 12 hours b ×3 +8 more

Supports a between-group comparison across 48 samples.

How we read this: 16 replicated groups read from 48 sample titles; they account for 48 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

+ 8 more — browse all 48 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

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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.