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LncRNAs coordinate doxycycline-induced gene expression response in human iPSCs (ATAC-seq)

GSE315440 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 341 samples Submitted 2026/04/01 Platform GPL34284
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 341 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Homo sapiens (human)
Samples
341 samples: 341 samples, each with a distinct title — no replicated groupsGroups 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)
Long non-coding RNAs are known to regulate gene expression. However, less is understood about the temporal dynamics of lncRNA regulation, particularly how they influence early, middle, and late gene expression. To investigate this, we generated 17 genetically defined, Doxycycline-inducible lncRNA transgene hiPSC lines and performed high-density time-course RNA-seq and ATAC-seq.
Read the full summary ↓
We observed that most lncRNA transgenes showed expected induction and subsequent changes in gene expression. However, the putative target genes of the different lncRNAs had substantial overlap, and control cell lines showed a similar set of induced genes, leading us to conclude that the substantial effect of doxycycline prevented identification of lncRNA-specific effects. Although doxycycline-induced gene expression changes have been reported previously, the large size of the current study allowed us to identify a highly reproducible doxycycline response gene signature (DRGS). We further observe that the DRGS occurs in most human cell lines tested with Dox exposure. Notably, the DRGS includes 18 endogenous lncRNAs that exhibit highly reproducible temporal regulation by Dox itself. Our results suggest these lncRNAs act synergistically as "co-response amplifiers" associated with the stress response; some are linked to different cell fates, such as epithelial-mesenchymal transition or nervous system development.
This dataset
Open GSE315440 in finder → Find more human ChIP / ATAC / CUT&Tag 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 GSE315440_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1394694 and SRA study SRP658654. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
341 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 341 sample titles: 341 distinct titles with little repetition. 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

+ 301 more — browse all 341 samples with per-sample file links →

Datasets on a similar topic

Search all human ChIP / ATAC / CUT&Tag datasets in GEO →

Share this dataset

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.