Inhibition of nonsense-mediated decay in TDP-43 deficient neurons reveals novel cryptic exons
RNA-seq (gene expression) · human · 22 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
- 22 samples: 11 conditions, mostly in duplicateGroups 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
- Inhibition of nonsense-mediated decay in TDP-43 deficient neurons reveals novel cryptic exonsbioRxiv : the preprint server for biology · 2025
Read the full summary ↓
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE307054_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1235234 and SRA study SRP569920. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 22 samples.
How we read this: 11 replicated groups read from 22 sample titles; they account for 22 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.
- GSM9214870 i3N: Control 1 Control
- GSM9214871 i3N: Control 2 Control
- GSM9214872 i3N: XRN1 KD 1 XRN1 KD
- GSM9214873 i3N: XRN1 KD 2 XRN1 KD
- GSM9214874 i3N: XRN1 KD + SMG6 KD 1 XRN1 KD + SMG6 KD
- GSM9214875 i3N: XRN1 KD + SMG6 KD 2 XRN1 KD + SMG6 KD
- GSM9214876 i3N: SMG6 KD + UPF1 KD 1 SMG6 KD + UPF1 KD
- GSM9214877 i3N: SMG6 KD + UPF1 KD 2 SMG6 KD + UPF1 KD
- GSM9214878 i3N: XRN1 KD + UPF1 KD 1 XRN1 KD + UPF1 KD
- GSM9214879 i3N: XRN1 KD + UPF1 KD 2 XRN1 KD + UPF1 KD
- GSM9214880 i3N: guide RNA control 1 guide RNA control
- GSM9214881 i3N: guide RNA control 2 guide RNA control
- GSM9214882 i3N: TDP-43 KD 1 TDP-43 KD
- GSM9214883 i3N: TDP-43 KD 2 TDP-43 KD
- GSM9214884 i3N: TDP-43 KD + XRN1 KD 1 TDP-43 KD + XRN1 KD
- GSM9214885 i3N: TDP-43 KD + XRN1 KD 2 TDP-43 KD + XRN1 KD
- GSM9214886 i3N: TDP-43 KD + XRN1 KD + SMG6 KD 1 TDP-43 KD + XRN1 KD + S…
- GSM9214887 i3N: TDP-43 KD + XRN1 KD + SMG6 KD 2 TDP-43 KD + XRN1 KD + S…
- GSM9214888 i3N: TDP-43 KD + SMG6 KD + UPF1 KD 1 TDP-43 KD + SMG6 KD + U…
- GSM9214889 i3N: TDP-43 KD + SMG6 KD + UPF1 KD 2 TDP-43 KD + SMG6 KD + U…
- GSM9214890 i3N: TDP-43 KD + XRN1 KD + UPF1 KD 1 TDP-43 KD + XRN1 KD + U…
- GSM9214891 i3N: TDP-43 KD + XRN1 KD + UPF1 KD 2 TDP-43 KD + XRN1 KD + U…
- GSE282668 TGF-β signaling promotes astroglial activation and TDP-43 proteinopathy in organoid models of frontotemporal lobar degeneration 54 samples shares tdp-43
- GSE254732 Inhibition of PCSK9 with evolocumab modulates lipoproteins and monocyte activation in high-risk ASCVD subjects 215 samples shares inhibition
- GSE275078 In vitro drug screening of RAF/MEK/ERK Inhibitors in combination with Autophagy inhibition in the context of two PDA Cell Lines 136 samples shares inhibition
- GSE273036 Multi-Omics Analysis and Molecular Subtypes Provide Potential Therapeutic Implications in Fumarate Hydratase-deficient Renal Cell Carcinoma 93 samples shares deficient
- GSE266219 Clinical and Immunological Responses to Combined JAK Inhibition and PD-1 immunotherapy for Lung Cancer Patients 79 samples shares inhibition
- GSE304126 CDK8 inhibition sequesters Med1 at EWS-FLI enhancers [RNA-Seq] 68 samples shares inhibition
- GSE222556 Neoadjuvant PARPi or Chemotherapy in Ovarian Cancer Informs Targeting Effector Treg Cells for Homologous-Recombination-Deficient Tumors [10x scRNA-seq] 67 samples shares deficient
- GSE268776 Multi-omics approaches reveal that Diffuse Midline Gliomas are susceptible to replication stress therapy and cholesterol biosynthesis inhibition [RNA-seq] 64 samples shares inhibition
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.