GEO series

Convection-enhanced delivery of dexamethasone in glioma models suppresses myeloid inflammation while avoiding systemic toxicities

GSE326006 Homo sapiens (human) Single-nucleus RNA-seq 21 samples Submitted 2026/07/07 Platform GPL34295Platform GPL24247

At a glance

Single-nucleus RNA-seq · human · 21 samples

What it is: Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue). 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)
Samples: 21 samples: 6 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.

Summary (written by the submitters)

Dexamethasone is widely used to control cerebral edema and inflammation in glioblastoma, but its benefits are limited by systemic toxicities and adverse prognostic associations. We evaluated local administration of dexamethasone via convection-enhanced delivery (CED) to maximize intratumoral anti-inflammatory effects by increasing local corticosteroid exposure while minimizing systemic exposure.

Read the full summary ↓

In two glioma mouse models, continuous intraparenchymal infusion of dexamethasone was well tolerated with no adverse effects. Pharmacokinetic analyses supported preferential intratumoral distribution and reduced systemic exposure with CED compared with systemic dosing. Single-nucleus RNA sequencing (snRNA-seq) and immunohistochemistry showed attenuation of glioma-associated inflammation with downregulation of reactive microglial/macrophage programs and reduced tumor-infiltrating myeloid cells with a morphology consistent with a less activated state. Experiments in human induced pluripotent stem cell (iPSC)–derived microglia confirmed that dexamethasone directly suppresses inflammatory gene expression, indicating a conserved mechanism across species. This inflammatory suppression was recapitulated in both immortalized microglial (HMC3) and macrophage (THP1) cell lines. These findings suggest that localized dexamethasone delivered by CED reprograms the glioma immune microenvironment and achieves control of inflammation without the systemic adverse effects associated with standard systemic dexamethasone therapy. This clinically translatable strategy may improve symptom management and provide a platform for integrating local immunomodulation with future glioblastoma therapies.

This dataset

Open GSE326006 in finder → Find more 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 GSE326006_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 PRJNA1442811 and SRA study SRP686740. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

6 conditions, mostly in triplicate

Control ×6 Systemic Dexamethasone ×3 CED Dexamethasone ×3 Dexamethasone ×3 LPS ×3 LPS+Dexamethasone ×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

GSM9618856 Systemic Dexamethasone 1 Systemic Dexamethasone
GSM9618857 Control 1 Control
GSM9618858 CED Dexamethasone 1 CED Dexamethasone
GSM9618859 Systemic Dexamethasone 2 Systemic Dexamethasone
GSM9618860 CED Dexamethasone 2 CED Dexamethasone
GSM9618861 Control 2 Control
GSM9618862 Systemic Dexamethasone 3 Systemic Dexamethasone
GSM9618863 Control 3 Control
GSM9618864 CED Dexamethasone 3 CED Dexamethasone
GSM9622070 Dexamethasone 1 Dexamethasone
GSM9622071 Dexamethasone 2 Dexamethasone
GSM9622072 Dexamethasone 3 Dexamethasone
GSM9622073 Control 1 Control
GSM9622074 Control 2 Control
GSM9622075 Control 3 Control
GSM9622076 LPS 1 LPS
GSM9622077 LPS 2 LPS
GSM9622078 LPS 3 LPS
GSM9622079 LPS+Dexamethasone 1 LPS+Dexamethasone
GSM9622080 LPS+Dexamethasone 2 LPS+Dexamethasone
GSM9622081 LPS+Dexamethasone 3 LPS+Dexamethasone

Datasets on a similar topic

GSE300754 CDK16 and CDK18 inhibition suppresses nuclear pore-mediated DNA repair and hepatocellular carcinoma 47 samples shares suppresses
GSE262088 Human-Specific Elimination of Epithelial Siglec-XII Suppresses the Risk of CRC Initiation and Progression 21 samples shares suppresses
GSE281781 MYC binding to nascent RNA suppresses innate immune signaling by R-loop-derived RNA-DNA hybrids 186 samples shares suppresses
GSE298580 Dual inhibition of FACT and RRM2 suppresses the progression of pancreatic ductal adenocarcinoma driven by the oncohistone H2BG53D 64 samples shares suppresses
GSE281611 Binding of MYC to nascent RNA suppresses innate immune signaling by R-loop-derived RNA-DNA hybrids [ChIP_Rx] 44 samples shares suppresses
GSE270756 PHF6 suppresses self-renewal of leukemic stem cells in AML 30 samples shares suppresses
GSE289626 RNA exonuclease REXO4 resolves m6A-marked R-loops and suppresses anti-tumor immunity 28 samples shares suppresses

Search all 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.