GEO series

Transcriptomic profiling of astrocytes under three extracellular acidification conditions

GSE330617 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2026/05/14 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 12 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: Mus musculus (mouse)
Samples: 12 samples: 3 × CON vs 3 × CO2 vs 3 × Lactic vs 3 × NaHCO3Groups 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)

Extracellular acidosis is a common feature of multiple pathological microenvironments, such as ischemia, tumors, inflammation, metabolic dysregulation, and tissue injury. Astrocytes are central regulators of brain homeostasis and are highly responsive to changes in extracellular pH. However, transcriptomic resources comparing different experimentally induced acidotic conditions in astrocytes remain limited.

Read the full summary ↓

Here, we generated an RNA sequencing dataset for the mouse astrocyte cell line C8-D1A exposed to three extracellular acidification-related conditions, including lactic acid treatment, 15% CO2 exposure, and NaHCO3-low medium, together with untreated controls. This dataset captures both shared and condition-specific transcriptomic responses of astrocytes under distinct extracellular acidification paradigms. Functional enrichment analyses highlighted biological pathways related to stress response, metabolism, inflammatory signaling, and cellular adaptation to extracellular acidification. This RNA-seq dataset provides a useful resource for studying astrocyte responses to different forms of extracellular acidotic stress and may facilitate the identification of common and distinct molecular programs associated with acidification-relevant cellular states.

This dataset

Open GSE330617 in finder → Find more mouse 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 GSE330617_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 PRJNA1463175 and SRA study SRP698306. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

3 × CON vs 3 × CO2 vs 3 × Lactic vs 3 × NaHCO3

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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

GSM9729361 CON_rep1 CON
GSM9729362 CON_rep2 CON
GSM9729363 CON_rep3 CON
GSM9729364 CO2_rep1 CO2
GSM9729365 CO2_rep2 CO2
GSM9729366 CO2_rep3 CO2
GSM9729367 Lactic_rep1 Lactic
GSM9729368 Lactic_rep2 Lactic
GSM9729369 Lactic_rep3 Lactic
GSM9729370 NaHCO3_rep1 NaHCO3
GSM9729371 NaHCO3_rep2 NaHCO3
GSM9729372 NaHCO3_rep3 NaHCO3

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