GSE277082
GSE GEOAging-linked deterioration of RNA metabolism destabilizes the stress response of neurons [RNASeq, RiboSeq]
Relations
Summary
Aging is one of the most prominent risk factors for neurodegeneration, yet the molecular mechanisms underlying the deterioration of old neurons are mostly unknown. To efficiently study neurodegeneration in the context of aging, we transdifferentiated primary human fibroblasts from aged healthy donors directly into neurons, which retained their aging markers. Here we show that aged neurons are broadly depleted of RNA-binding proteins, especially spliceosome components. Intriguingly, splicing proteins â like the dementia and ALS-associated protein TDP-43 â mislocalize to the cytoplasm in aged neurons, which leads to widespread alternative splicing. Cytoplasmic spliceosome components typically are recruited to stress granules, but aged neurons suffer from chronic stress that prevents this sequestration. We link chronic stress to the malfunctioning ubiquitylation machinery, poor HSP90α chaperone activity, and the failure to respond to new stress events. Together our data demonstrates that aging-linked deterioration of RNA biology is a key driver of poor resiliency in aged neurons.
Overall Design
Riboseq of isogenic transdifferentiated and iPSC-derived neurons; bulk RNA was isolated from untreated cells whereas RNA for ribosomal footprinting (to calculate translation efficiency) was derived from cells treated with cycloheximide, which locks RNA on ribosomes
Analysis (2 steps)
View Data Processing- Riboseq data was analyzed as described previously; see Tirosh et al.
- 2015 doi:10.1371/journal.ppat.1005288
Supplementary Files (2)
GEO Samples (8)
SRA Experiments (8) and Runs (8)
Total: 7181 MBSample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR30652209 | 8571315 | 865702815 | 317.05 | rnaseq_NGN_rep1_S27_L001_R1_001.fastq.gz, SRR30652209, SRR30652209.li… | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR30652208 | 14626787 | 1477305487 | 536.66 | rnaseq_NGN_rep2_S28_L001_R1_001.fastq.gz, SRR30652208, SRR30652208.li… | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR30652207 | 21772592 | 2199031792 | 804.29 | rp_NGN_rep1_S19_L001_R1_001.fastq.gz, SRR30652207, SRR30652207.lite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR30652206 | 18927010 | 1911628010 | 705.25 | rp_NGN_rep2_S20_L001_R1_001.fastq.gz, SRR30652206, SRR30652206.lite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR30652205 | 14395238 | 1453919038 | 529.78 | rnaseq_NK_rep1_S29_L001_R1_001.fastq.gz, SRR30652205, SRR30652205.lite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR30652204 | 73742726 | 7448015326 | 2611.52 | rnaseq_NK_rep2_S30_L001_R1_001.fastq.gz, SRR30652204, SRR30652204.lite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR30652203 | 25052479 | 2530300379 | 940.67 | rp_NK_rep1_S21_L001_R1_001.fastq.gz, SRR30652203, SRR30652203.lite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR30652202 | 19845818 | 2004427618 | 735.75 | rp_NK_rep2_S22_L001_R1_001.fastq.gz, SRR30652202, SRR30652202.lite | SRA |
Linked Publications (1)
Data Files (8)
| Accession | File Name | Stored Type | Output Type | Mapping Assembly | Size | Download | |
|---|---|---|---|---|---|---|---|
| — | rp_NGN_rep1_S19_L001_R1_001.fastq.gz | OTHER | 804.3 MB | link | |||
| — | rp_NGN_rep2_S20_L001_R1_001.fastq.gz | OTHER | 705.2 MB | link | |||
| — | rp_NK_rep1_S21_L001_R1_001.fastq.gz | OTHER | 940.7 MB | link | |||
| — | rp_NK_rep2_S22_L001_R1_001.fastq.gz | OTHER | 735.8 MB | link | |||
| — | rnaseq_NGN_rep1_S27_L001_R1_001.fastq.gz | RNA-Seq | 317.0 MB | link | |||
| — | rnaseq_NGN_rep2_S28_L001_R1_001.fastq.gz | RNA-Seq | 536.7 MB | link | |||
| — | rnaseq_NK_rep1_S29_L001_R1_001.fastq.gz | RNA-Seq | 529.8 MB | link | |||
| — | rnaseq_NK_rep2_S30_L001_R1_001.fastq.gz | RNA-Seq | 2.6 GB | link |