GEO series

Time-Resolved Analysis Reveals FEN1 as a Crucial Factor of Circadian Transcriptome Dynamics and Core Cellular Homeostasis in HEK 293T cell

GSE308811 Homo sapiens (human) RNA-seq (gene expression) 36 samples Submitted 2026/03/04 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 36 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: 36 samples: 12 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: Temporal dynamics and functional annotation of transcriptome rhythmicity in HEK293T cellsPloS one · 2026

Summary (written by the submitters)

Circadian rhythms orchestrate genome-wide transcriptional oscillations to coordinate cellular homeostasis. While the core clock machinery has been extensively characterized, its integration with other critical biological processes, such as the DNA damage response and cell cycle control, remains incompletely understood. Here, we identify the DNA replication and repair nuclease FEN1 as a critical modulator of circadian transcriptome dynamics in human cells.

Read the full summary ↓

Time-series RNA-seq across six circadian time points in synchronized HEK293T cells revealed that FEN1 depletion induces widespread reprogramming of rhythmic gene expression, with over 30% of oscillatory transcripts exhibiting loss or gain of rhythmicity, phase shifts, or amplitude changes. Notably, reprogrammed genes were enriched in cell cycle, DNA damage response, and cellular senescence pathways. Systematic phase set enrichment analysis uncovered coordinated delays and inversions in G1/S checkpoint regulators and metabolic genes, disrupting temporal coherence. Despite retention of rhythmicity in core clock genes, amplitude attenuation and phase advances were observed, indicating compromised oscillatory stability. Functional validation demonstrated reduced S phase entry, G1 accumulation, and accelerated senescence in FEN1 knockdown cells, in line with transcriptomic predictions. qPCR analysis confirmed altered expression of representative target genes. These findings uncover an unrecognized role for FEN1 in sustaining circadian transcriptional architecture and reveal its broader impact on cell cycle control and aging programs.

Published in

Temporal dynamics and functional annotation of transcriptome rhythmicity in HEK293T cells

Sun Y, Dong H, Ge F et al. · PloS one 2026 · PMID 41746989 · doi:10.1371/journal.pone.0343991

This dataset

Open GSE308811 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 GSE308811_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 PRJNA1332738 and SRA study SRP624829. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41746989) ↗

Study design

12 conditions, mostly in triplicate

2WTCT0, ×3 2WTCT4, ×3 2WTCT8, ×3 2WTCT12, ×3 2WTCT16, ×3 2WTCT20, ×3 2KOCT0, ×3 2KOCT4, ×3 +4 more

Supports a between-group comparison across 36 samples.

How we read this: 12 replicated groups read from 36 sample titles; they account for 36 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

GSM9253491 2WTCT0,rep1 2WTCT0,
GSM9253492 2WTCT0,rep2 2WTCT0,
GSM9253493 2WTCT0,rep3 2WTCT0,
GSM9253494 2WTCT4,rep1 2WTCT4,
GSM9253495 2WTCT4,rep2 2WTCT4,
GSM9253496 2WTCT4,rep3 2WTCT4,
GSM9253497 2WTCT8,rep1 2WTCT8,
GSM9253498 2WTCT8,rep2 2WTCT8,
GSM9253499 2WTCT8,rep3 2WTCT8,
GSM9253500 2WTCT12,rep1 2WTCT12,
GSM9253501 2WTCT12,rep2 2WTCT12,
GSM9253502 2WTCT12,rep3 2WTCT12,
GSM9253503 2WTCT16,rep1 2WTCT16,
GSM9253504 2WTCT16,rep2 2WTCT16,
GSM9253505 2WTCT16,rep3 2WTCT16,
GSM9253506 2WTCT20,rep1 2WTCT20,
GSM9253507 2WTCT20,rep2 2WTCT20,
GSM9253508 2WTCT20,rep3 2WTCT20,
GSM9268689 2KOCT0,rep1 2KOCT0,
GSM9268690 2KOCT0,rep2 2KOCT0,
GSM9268691 2KOCT0,rep3 2KOCT0,
GSM9268692 2KOCT4,rep1 2KOCT4,
GSM9268693 2KOCT4,rep2 2KOCT4,
GSM9268694 2KOCT4,rep3 2KOCT4,
GSM9268695 2KOCT8,rep1 2KOCT8,
GSM9268696 2KOCT8,rep2 2KOCT8,
GSM9268697 2KOCT8,rep3 2KOCT8,
GSM9268698 2KOCT12,rep1 2KOCT12,
GSM9268699 2KOCT12,rep2 2KOCT12,
GSM9268700 2KOCT12,rep3 2KOCT12,
GSM9268701 2KOCT16,rep1 2KOCT16,
GSM9268702 2KOCT16,rep2 2KOCT16,
GSM9268703 2KOCT16,rep3 2KOCT16,
GSM9268704 2KOCT20,rep1 2KOCT20,
GSM9268705 2KOCT20,rep2 2KOCT20,
GSM9268706 2KOCT20,rep3 2KOCT20,

Datasets on a similar topic

GSE315903 Temporal dynamics and functional annotation of transcriptome rhythmicity in HEK293T cells 39 samples shares 293t, hek, dynamics
GSE316070 A Prevalent Disease-Associated SNP in the Human ID3 Gene Regulates E-Protein Activity and Cellular Proliferation [HEK293T RNA-Seq] 9 samples shares 293t, hek, cellular
GSE317890 Transcriptomic profiling of interferon responses induced by IVT sgRNAs in CRISPRi HEK293T cells 360 samples shares 293t, hek
GSE335700 RNA sequencing of vtRNA-knockout HEK293T cell lines 36 samples shares 293t, hek
GSE242550 SRSF1 knockdown in HEK293T cells with ionizing radiation 20 samples shares 293t, hek
GSE247514 Transcriptional response induced by knockdown of HUWE1 in human HEK293T cells 20 samples shares 293t, hek
GSE266017 Effect of DHX29 depletion on mRNA stability in HEK293T cells 18 samples shares 293t, hek
GSE270586 The specificity of gene activation was revealed by RNA-seq in the HEK293T cells transfected with the dCasMINI-VPR or dhpCasMINI-VPR system targeting IL1RN [RNA-seq] 18 samples shares 293t, hek

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.