GEO series

Yin Yang 1 and guanine quadruplexes protect dopaminergic neurons from cellular stress via transmissive dormancy [TG timeline RNA-seq]

GSE254139 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2024/10/28 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 24 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: 24 samples: 6 conditions, mostly with about 4 replicates eachGroups 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: Yin Yang 1 and guanine quadruplexes protect dopaminergic neurons from cellular stress via transmissive dormancyNature communications · 2024

Summary (written by the submitters)

Neurons deploy diverse adaptive strategies to ensure survival and neurotransmission amid cellular stress. Yet, when these adaptive pathways are overwhelmed, functional impairment or neurodegeneration follow. Herein we report a scenario where stressed neurons actively adopt a state of transmissive dormancy, despite rapid activation of stress response pathways, as a terminal protective measure.

Read the full summary ↓

Examination of dopaminergic neurons surviving severe cellular stress, revealed decreased spontaneous activity accompanied by dynamic control of dopamine metabolism through the Yin Yang 1 (YY1) transcriptional regulator. Under conditions of ionic imbalance or oxidative stress, YY1 promotes expression of the SLC18A2 transporter with the capacity to enhance sequestration of dopamine into transport vesicles. Subsequent DNA damage represses the rate-limiting enzyme in dopamine synthesis, tyrosine hydroxylase (TH), through YY1 mediated stabilization of an intronic guanine quadruplex. This cascade has the potential to drive circuit inactivation and safeguard neurons by minimizing the toxic accumulation of cytosolic dopamine and reducing the energetic expenditure associated with cellular depolarization. In essence, neurons appear to actively prioritize viability over functionality.

Published in

Yin Yang 1 and guanine quadruplexes protect dopaminergic neurons from cellular stress via transmissive dormancy

Zuurbier KR, Fonseca RS, Arneaud SLB et al. · Nature communications 2024 · PMID 39632864 · doi:10.1038/s41467-024-54958-9

This dataset

Open GSE254139 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 GSE254139_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 PRJNA1068619 and SRA study SRP485774. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39632864) ↗

Study design

6 conditions, mostly with about 4 replicates each

Diff LUHMES, DMSO, 3hr, ×4 Diff LUHMES, TG, 3hr, ×4 Diff LUHMES, DMSO, 6hr, ×4 Diff LUHMES, TG, 6hr, ×4 Diff LUHMES, DMSO, 24hr, ×4 Diff LUHMES, TG, 24hr, ×4

Supports a between-group comparison across 24 samples.

How we read this: 6 replicated groups read from 24 sample titles; they account for 24 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

GSM8034841 Diff LUHMES, DMSO, 3hr, rep1 Diff LUHMES, DMSO, 3hr,
GSM8034842 Diff LUHMES, DMSO, 3hr, rep2 Diff LUHMES, DMSO, 3hr,
GSM8034843 Diff LUHMES, DMSO, 3hr, rep3 Diff LUHMES, DMSO, 3hr,
GSM8034844 Diff LUHMES, DMSO, 3hr, rep4 Diff LUHMES, DMSO, 3hr,
GSM8034845 Diff LUHMES, TG, 3hr, rep1 Diff LUHMES, TG, 3hr,
GSM8034846 Diff LUHMES, TG, 3hr, rep2 Diff LUHMES, TG, 3hr,
GSM8034847 Diff LUHMES, TG, 3hr, rep3 Diff LUHMES, TG, 3hr,
GSM8034848 Diff LUHMES, TG, 3hr, rep4 Diff LUHMES, TG, 3hr,
GSM8034849 Diff LUHMES, DMSO, 6hr, rep1 Diff LUHMES, DMSO, 6hr,
GSM8034850 Diff LUHMES, DMSO, 6hr, rep2 Diff LUHMES, DMSO, 6hr,
GSM8034851 Diff LUHMES, DMSO, 6hr, rep3 Diff LUHMES, DMSO, 6hr,
GSM8034852 Diff LUHMES, DMSO, 6hr, rep4 Diff LUHMES, DMSO, 6hr,
GSM8034853 Diff LUHMES, TG, 6hr, rep1 Diff LUHMES, TG, 6hr,
GSM8034854 Diff LUHMES, TG, 6hr, rep2 Diff LUHMES, TG, 6hr,
GSM8034855 Diff LUHMES, TG, 6hr, rep3 Diff LUHMES, TG, 6hr,
GSM8034856 Diff LUHMES, TG, 6hr, rep4 Diff LUHMES, TG, 6hr,
GSM8034857 Diff LUHMES, DMSO, 24hr, rep1 Diff LUHMES, DMSO, 24hr,
GSM8034858 Diff LUHMES, DMSO, 24hr, rep2 Diff LUHMES, DMSO, 24hr,
GSM8034859 Diff LUHMES, DMSO, 24hr, rep3 Diff LUHMES, DMSO, 24hr,
GSM8034860 Diff LUHMES, DMSO, 24hr, rep4 Diff LUHMES, DMSO, 24hr,
GSM8034861 Diff LUHMES, TG, 24hr, rep1 Diff LUHMES, TG, 24hr,
GSM8034862 Diff LUHMES, TG, 24hr, rep2 Diff LUHMES, TG, 24hr,
GSM8034863 Diff LUHMES, TG, 24hr, rep3 Diff LUHMES, TG, 24hr,
GSM8034864 Diff LUHMES, TG, 24hr, rep4 Diff LUHMES, TG, 24hr,

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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.