GEO series

Effect of TNFα and RELA inhibition on gene expression in human PDAC cells

GSE268743 Homo sapiens (human) Single-cell RNA-seq 28 samples Submitted 2024/10/25 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 28 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Homo sapiens (human)
Topic: Pancreatic cancerThis series is part of our curated briefing on it.
Samples: 28 samples: 28 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.
Paper: Actin networks modulate heterogeneous NF-κB dynamics in response to TNFαeLife · 2024

Summary (written by the submitters)

The canonical NF-κB transcription factor RELA is a master regulator of immune and stress responses and is upregulated in PDAC tumours. Here, we characterised previously unknown endogenous RELA-GFP dynamics in PDAC cell lines by live single cell imaging, which revealed rapid, sustained and non-oscillatory nuclear RELA following TNFα stimulation.

Read the full summary ↓

Using Bayesian analysis of single cell datasets with variation in nuclear RELA, we predicted that RELA heterogeneity in PDAC cell lines is dependent on F-actin dynamics. Using RNA-seq, we identified the actin regulators NUAK2 and ARHGAP31 as transcriptionally regulated by RELA. In turn, NUAK2 or ARHGAP31 siRNA depletion downregulates TNFα-stimulated RELA nuclear localisation in PDAC cells, establishing a novel negative feedback loop regulating RELA activation by TNFα. We identify an additional actin-independent feedback loop involving RELB, which suppresses TNFα-mediated RELA nuclear localisation following RELA mediated upregulation of RELB. Taken together, we provide computational and experimental support for interdependence between the F-actin network and RELA translocation dynamics in PDAC.

Published in

Actin networks modulate heterogeneous NF-κB dynamics in response to TNFα

Butera F, Sero JE, Dent LG et al. · eLife 2024 · PMID 39110005 · doi:10.7554/eLife.86042

This dataset

Open GSE268743 in finder → Find more human RNA-seq datasets → Pancreatic 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 GSE268743_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1118415 and SRA study SRP510931. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39110005) ↗

Study design

28 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 28 sample titles: 28 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

GSM8298264 MIA PaCa2 cells, 1 hr DMSO treatment
GSM8298265 MIA PaCa2 cells, 5 hr DMSO treatment
GSM8298266 MIA PaCa2 cells, 1 hr 0.01 ng/ml TNF treatment
GSM8298267 MIA PaCa2 cells, 5 hr 0.01 ng/ml TNF treatment
GSM8298268 MIA PaCa2 cells, 1 hr 0.1 ng/ml TNF treatment
GSM8298269 MIA PaCa2 cells, 5 hr 0.1 ng/ml TNF treatment
GSM8298270 MIA PaCa2 cells, 1 hr 10 ng/ml TNF treatment
GSM8298271 MIA PaCa2 cells, 5 hr 10 ng/ml TNF treatment
GSM8298272 MIA PaCa2 cells, 1 hr DMSO + 1 µg/ml dox treatment
GSM8298273 MIA PaCa2 cells, 5 hr DMSO + 1 µg/ml dox treatment
GSM8298274 MIA PaCa2 cells, 1 hr 0.1 ng/ml TNF + 1 µg/ml dox treatment
GSM8298275 MIA PaCa2 cells, 5 hr 0.1 ng/ml TNF + 1 µg/ml dox treatment
GSM8298276 MIA PaCa2 cells, 1 hr 10 ng/ml TNF + 1 µg/ml dox treatment
GSM8298277 MIA PaCa2 cells, 5 hr 10 ng/ml TNF + 1 µg/ml dox treatment
GSM8298278 PANC1 cells, 1 hr DMSO treatment
GSM8298279 PANC1 cells, 5 hr DMSO treatment
GSM8298280 PANC1 cells, 1 hr 0.01 ng/ml TNF treatment
GSM8298281 PANC1 cells, 5 hr 0.01 ng/ml TNF treatment
GSM8298282 PANC1 cells, 1 hr 0.1 ng/ml TNF treatment
GSM8298283 PANC1 cells, 5 hr 0.1 ng/ml TNF treatment
GSM8298284 PANC1 cells, 1 hr 10 ng/ml TNF treatment
GSM8298285 PANC1 cells, 5 hr 10 ng/ml TNF treatment
GSM8298286 PANC1 cells, 1 hr DMSO + 1 µg/ml dox treatment
GSM8298287 PANC1 cells, 5 hr DMSO + 1 µg/ml dox treatment
GSM8298288 PANC1 cells, 1 hr 0.1 ng/ml TNF + 1 µg/ml dox treatment
GSM8298289 PANC1 cells, 5 hr 0.1 ng/ml TNF + 1 µg/ml dox treatment
GSM8298290 PANC1 cells, 1 hr 10 ng/ml TNF + 1 µg/ml dox treatment
GSM8298291 PANC1 cells, 5 hr 10 ng/ml TNF + 1 µg/ml dox treatment

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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.