GEO series

Gene expression profiling of HBEpCs and Caco-2 cells during infection with WT SARS-CoV-2 or a recombinant SARS-CoV-2 deficient in PLpro deISGylation activity

GSE308448 Homo sapiens (human) RNA-seq (gene expression) 21 samples Submitted 2026/05/08 Platform GPL34284

At a glance

RNA-seq (gene expression) · human · 21 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: 21 samples: 6 conditions, mostly with about 4 replicates eachGroups 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)

Interferon-stimulated gene 15 (ISG15) regulates diverse cellular processes, including antiviral immunity, through its conjugation to proteins, a process known as ISGylation. Several pathogens, including SARS-CoV-2, subvert ISGylation by encoding deISGylating enzymes. However, the direct targets and physiological consequences of coronaviral deISGylation remain poorly defined.

Read the full summary ↓

Here, we engineered a recombinant SARS-CoV-2 harboring a mutant Nsp3 (Nsp3mut) with impaired papain-like protease (PLpro) deISGylating activity. Caco-2 and human bronchial epithelial (HBEpC) cells were infected with either wild-type or Nsp3mut SARS-CoV-2. Comparative transcriptomic profiling revealed that Nsp3mut infection led to a stronger induction of IFN- and ISG-related gene signatures compared to wild-type virus infection in both cell types. These results show that loss of PLpro-mediated deISGylation restores efficient antiviral innate immune responses during SARS-CoV-2 infection.

This dataset

Open GSE308448 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 GSE308448_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 PRJNA1330611 and SRA study SRP621813. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

6 conditions, mostly with about 4 replicates each

Caco-2 cells, Mock, 20 h, biol ×4 Caco-2 cells, WT, 20 h, biol ×4 Caco-2 cells, Nsp3mut, 20 h, biol ×4 HBEpCs, Mock, 20 h, biol ×3 HBEpCs, WT, 20 h, biol ×3 HBEpCs, Nsp3mut, 20 h, biol ×3

Supports a between-group comparison across 21 samples.

How we read this: 6 replicated groups read from 21 sample titles; they account for 21 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

GSM9245722 Caco-2 cells, Mock, 20 h, biol rep 1 Caco-2 cells, Mock, 20 …
GSM9245723 Caco-2 cells, Mock, 20 h, biol rep 2 Caco-2 cells, Mock, 20 …
GSM9245724 Caco-2 cells, Mock, 20 h, biol rep 3 Caco-2 cells, Mock, 20 …
GSM9245725 Caco-2 cells, Mock, 20 h, biol rep 4 Caco-2 cells, Mock, 20 …
GSM9245726 Caco-2 cells, WT, 20 h, biol rep 1 Caco-2 cells, WT, 20 h,…
GSM9245727 Caco-2 cells, WT, 20 h, biol rep 2 Caco-2 cells, WT, 20 h,…
GSM9245728 Caco-2 cells, WT, 20 h, biol rep 3 Caco-2 cells, WT, 20 h,…
GSM9245729 Caco-2 cells, WT, 20 h, biol rep 4 Caco-2 cells, WT, 20 h,…
GSM9245730 Caco-2 cells, Nsp3mut, 20 h, biol rep 1 Caco-2 cells, Nsp3mut, …
GSM9245731 Caco-2 cells, Nsp3mut, 20 h, biol rep 2 Caco-2 cells, Nsp3mut, …
GSM9245732 Caco-2 cells, Nsp3mut, 20 h, biol rep 3 Caco-2 cells, Nsp3mut, …
GSM9245733 Caco-2 cells, Nsp3mut, 20 h, biol rep 4 Caco-2 cells, Nsp3mut, …
GSM9245734 HBEpCs, Mock, 20 h, biol rep 1 HBEpCs, Mock, 20 h, biol
GSM9245735 HBEpCs, Mock, 20 h, biol rep 2 HBEpCs, Mock, 20 h, biol
GSM9245736 HBEpCs, Mock, 20 h, biol rep 3 HBEpCs, Mock, 20 h, biol
GSM9245737 HBEpCs, WT, 20 h, biol rep 1 HBEpCs, WT, 20 h, biol
GSM9245738 HBEpCs, WT, 20 h, biol rep 2 HBEpCs, WT, 20 h, biol
GSM9245739 HBEpCs, WT, 20 h, biol rep 3 HBEpCs, WT, 20 h, biol
GSM9245740 HBEpCs, Nsp3mut, 20 h, biol rep 1 HBEpCs, Nsp3mut, 20 h, …
GSM9245741 HBEpCs, Nsp3mut, 20 h, biol rep 2 HBEpCs, Nsp3mut, 20 h, …
GSM9245742 HBEpCs, Nsp3mut, 20 h, biol rep 3 HBEpCs, Nsp3mut, 20 h, …

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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.