← BioTransfer GEO Dataset Finder
GEO series

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

GSE316178 Homo sapiens (human) RNA-seq (gene expression) 658 samples Submitted 2026/04/01 Platform GPL34284
At a glance

RNA-seq (gene expression) · human · 658 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
658 samples: 658 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 GSE316178 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 GSE316178_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 PRJNA1394694 and SRA study SRP658654. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
658 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 the first 400 of 658 sample titles: 400 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

+ 618 more — browse all 658 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq 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.