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Effect of CA3 overexpression on signalling pathways in different cell lines

GSE311117 Homo sapiens (human) RNA-seq (gene expression) 32 samples Submitted 2025/11/29 Platform GPL30173
At a glance

RNA-seq (gene expression) · human · 32 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
32 samples: 10 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
Carbonic Anhydrase 3 Overexpression Modulates Signalling Pathways Associated with Cellular Stress Resilience and ProteostasisInternational journal of molecular sciences · 2025
Summary (written by the submitters)
Carbonic Anhydrase 3 (CA3) was an understudied member of the carbonic anhydrase family. It is highly expressed in muscle tissue and contains two surface-exposed cysteine residues, which can undergo glutathionylation. The redox modification protects cells under oxidative stress. Recent studies have shown that CA3 interacts with Bcl-2–Associated Athanogene 3 (BAG3) and squalene epoxidase (SQLE), implicating CA3 in the pathogenesis of myasthenia gravis and non-alcoholic fatty liver disease.
Read the full summary ↓
CA3 overexpression has also been reported to reduce hypoxia-induced apoptosis in cardiomyocytes. In this study, we performed RNA-seq profiling on HEK293T, MDA-MB-231, and SVCT cell lines following CA3 overexpression. HEK293T cells were analyzed only under normoxic conditions, whereas MDA-MB-231 and SVCT cells were cultured under both normoxia and hypoxia.
Published in
Carbonic Anhydrase 3 Overexpression Modulates Signalling Pathways Associated with Cellular Stress Resilience and Proteostasis
Yu Y, Anugraham M, Blick T et al. · International journal of molecular sciences 2025 · PMID 41465490 · doi:10.3390/ijms262412064
This dataset
Open GSE311117 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 GSE311117_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 PRJNA1368701 and SRA study SRP648390. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41465490) ↗
Study design
10 conditions, mostly in triplicate
HEK293T, CA3 overexpression, normoxia, repeat ×4 HEK293T, vector control, normoxia, repeat ×4 MDA-MB-231, CA3 overexpression, hypoxia, repe… ×3 MDA-MB-231, vector control, hypoxia, repeat ×3 MDA-MB-231, CA3 overexpression, normoxia, rep… ×3 MDA-MB-231, vector control, normoxia, repeat ×3 SVCT, CA3 overexpression, hypoxia, repeat ×3 SVCT, vector control, hypoxia, repeat ×3 +2 more

Supports a case/control comparison: 16 samples read as cases, 16 as controls.

How we read this: 10 replicated groups read from 32 sample titles; they account for 32 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
Datasets on a similar topic

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