GEO series

Effects of overexpression of a C9orf72 repeat expansion linked to GFP, or a GFP control in human HEK293 cells, in the presence or absence of the EIF2B activator DNL343.

GSE281958 Homo sapiens (human) RNA-seq (gene expression) 23 samples Submitted 2025/06/30 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 23 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: 23 samples: 6 × GFP, DMSO, vs 6 × GFP, DNL343, vs 6 × (G4C2)71-GFP, DNL343, vs 5 × (G4C2)71-GFP, DMSO,Groups 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)

Neuronal TDP-43 aggregates are a hallmark ALS pathology. The integrated stress response (ISR) occurs downstream of TDP-43 pathology and may exacerbate TDP-43 aggregation and neurodegeneration. Here we assessed the effects of overexpression of a GFP-taggted C9orf72 repeat expansion in HEK293 cells on the transcriptome, in the presence or ascence of the EIF2B activiting small molecule DNL343. Expression of (G4C2)71-GFP upregulated most of the pre-defined ISR genes compared to GFP expression alone. These transcriptional changes were largely corrected by DNL343 treatment.

This dataset

Open GSE281958 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 GSE281958_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 PRJNA1186322 and SRA study SRP545345. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

6 × GFP, DMSO, vs 6 × GFP, DNL343, vs 6 × (G4C2)71-GFP, DNL343, vs 5 × (G4C2)71-GFP, DMSO,

Supports a between-group comparison across 23 samples.

How we read this: 4 replicated groups read from 23 sample titles; they account for 23 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

GSM8633542 GFP, DMSO, replicate 1 GFP, DMSO,
GSM8633543 (G4C2)71-GFP, DMSO, replicate 1 (G4C2)71-GFP, DMSO,
GSM8633544 GFP, DNL343, replicate 1 GFP, DNL343,
GSM8633545 (G4C2)71-GFP, DNL343, replicate 1 (G4C2)71-GFP, DNL343,
GSM8633546 GFP, DMSO, replicate 2 GFP, DMSO,
GSM8633547 (G4C2)71-GFP, DMSO, replicate 2 (G4C2)71-GFP, DMSO,
GSM8633548 GFP, DNL343, replicate 2 GFP, DNL343,
GSM8633549 (G4C2)71-GFP, DNL343, replicate 2 (G4C2)71-GFP, DNL343,
GSM8633550 GFP, DMSO, replicate 3 GFP, DMSO,
GSM8633551 (G4C2)71-GFP, DMSO, replicate 3 (G4C2)71-GFP, DMSO,
GSM8633552 GFP, DNL343, replicate 3 GFP, DNL343,
GSM8633553 (G4C2)71-GFP, DNL343, replicate 3 (G4C2)71-GFP, DNL343,
GSM8633554 GFP, DMSO, replicate 4 GFP, DMSO,
GSM8633555 GFP, DNL343, replicate 4 GFP, DNL343,
GSM8633556 (G4C2)71-GFP, DNL343, replicate 4 (G4C2)71-GFP, DNL343,
GSM8633557 GFP, DMSO, replicate 5 GFP, DMSO,
GSM8633558 (G4C2)71-GFP, DMSO, replicate 5 (G4C2)71-GFP, DMSO,
GSM8633559 GFP, DNL343, replicate 5 GFP, DNL343,
GSM8633560 (G4C2)71-GFP, DNL343, replicate 5 (G4C2)71-GFP, DNL343,
GSM8633561 GFP, DMSO, replicate 6 GFP, DMSO,
GSM8633562 (G4C2)71-GFP, DMSO, replicate 6 (G4C2)71-GFP, DMSO,
GSM8633563 GFP, DNL343, replicate 6 GFP, DNL343,
GSM8633564 (G4C2)71-GFP, DNL343, replicate 6 (G4C2)71-GFP, DNL343,

Datasets on a similar topic

GSE281957 Effects of overexpression of GFP-TDP-43, GFP-TDP-43(86-414) or GFP in human H4 cells, in the presence or absence of the EIF2B activator DNL343. 47 samples shares dnl343, eif2b, gfp, overexpression, activator
GSE281960 Investigational eIF2B activator DNL343 modulates the Integrated Stress Response in Preclinical Models of TDP-43 Pathology. 70 samples shares dnl343, eif2b, activator
GSE260781 Effect of VGLL2-NCOA2, YAP5SA and GFP overexpression on chromatin accessibility profiling in HEK293T cells (ATAC-Seq) 6 samples shares hek293, gfp, overexpression
GSE302320 C9orf72 hexanucleotide repeat expansions impair microglial response in models of ALS 44 samples shares c9orf72, expansion
GSE302295 C9orf72 hexanucleotide repeat expansions impair microglial response in models of ALS [RNA] 30 samples shares c9orf72, expansion
GSE247790 Aberrant splicing exonizes C9ORF72 repeat expansion in ALS/FTD 18 samples shares c9orf72, expansion
GSE87198 RNA sequencing quantitative analysis of RNA editing levels in ADAR1, ADAR2, AIMP2 overexpression and wild type HEK293 cells 17 samples shares hek293, overexpression
GSE302319 C9orf72 hexanucleotide repeat expansions impair microglial response in models of ALS [scRNA] 14 samples shares c9orf72, expansion

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