GEO series

Long Reads RNAseq reveals an isoform switching pattern in healthy microglial cell lines exposed to radiotherapy.

GSE336257 Homo sapiens (human) RNA-seq (gene expression) 6 samples Submitted 2026/08/06 Platform GPL26167

At a glance

RNA-seq (gene expression) · human · 6 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: 6 samples: 6 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.

Summary (written by the submitters)

Background/Objectives: Radiotherapy (RT) is a fundamental treatment for brain tumors but often leads to long-term neurotoxicity, partly caused by microglial dysfunction. In this study, we used long-read RNA sequencing (LR-RNA-seq) to map the isoform-specific transcriptome of human microglial HMC3 cells after RT exposure Methods: HMC3 Microglial cell line was treated with standard radiotherapy and, after RNA extraction and library preparation, long reads RNAseq has been carried out.

Read the full summary ↓

Further bioinformatic analyses allowed to investigate on the isoform switching pattern after radiation therapy exposure. Results: Gene-level analysis found 591 differentially expressed genes, with increased activity in PI3K/AKT signaling pathways and decreased translation-related processes. Isoform-level analysis uncovered 827 significant isoform switching events across 420 genes, often involving shifts from protein-coding transcripts to non-coding variants. Functional annotation showed that most isoform switches resulted in the loss of open reading frames and protein domains, especially in ribosomal proteins and translation machinery components

This dataset

Open GSE336257 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 GSE336257_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 PRJNA1481156 and SRA study SRP711848. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

6 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 6 sample titles: 6 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

GSM9830911 HMC3, Control, Replicate 1, 24h
GSM9830912 HMC3, Control, Replicate 2, 24h
GSM9830913 HMC3, Control, Replicate 3, 24h
GSM9830914 HMC3, Radiotherapy, Replicate 1, 24h
GSM9830915 HMC3, Radiotherapy, Replicate 2, 24h
GSM9830916 HMC3, Radiotherapy, Replicate 3, 24h

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GSE254145 Multidimensional analysis of patient-matched primary and recurrent glioblastoma identifies microglial FCGR1A (CD64) and other FCGRs as contributors of tumor recurrence [seq] 79 samples shares microglial
GSE285352 Alternate isoforms of IRF7 Differentially Regulate Interferon Expression 74 samples shares isoform
GSE327711 GPR34 regulation of disease-associated microglial states in iMGL 60 samples shares microglial
GSE248094 Systematic characterization of single-cell full-length RNA isoforms in human colorectal cancer 51 samples shares isoform
GSE231555 Splicing and gene expression changes in cell lines treated with splicing switching oligonucleotide targeting TRA2B 46 samples shares switching

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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.