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Hypoxia dysregulates circadian rhythm and causes synapse elimination defects in astrocytes

GSE255588 Homo sapiens (human) RNA-seq (gene expression) 28 samples Submitted 2025/02/12 Platform GPL20301
At a glance

RNA-seq (gene expression) · human · 28 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
28 samples: 28 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)
In this study, we used human cortical organoids (hCOs) derived from induced pluripotent stem cells (iPSCs) to examine how hypoxia exposure interferes with astrocyte synapse engulfment at 6 months in culture and 10 months in culture, equivalent to mid fetal- or neonatal-equivalent stages of development, respectively. We identified that hypoxia inhibits the synaptosome engulfment by human astrocytes at both developmental stages, with a more pronounced phenotype in 10 months astrocytes.
Read the full summary ↓
Transcriptional analyses revealed disruptions in circadian rhythm pathways in hypoxic astrocytes, but not neurons, and PER2 luciferase assays (PER2::LUC) validated the presence of circadian rhythms and their disruption by hypoxia in intact hCOs, with more pronounced rhythms in 10 months hCOs.
This dataset
Open GSE255588 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 GSE255588_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 PRJNA1075676 and SRA study SRP489403. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
28 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 28 sample titles: 28 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
Datasets on a similar topic

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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.