GEO series

A novel noninvasive murine model of neonatal hypoxic ischemic encephalopathy demonstrates developmental delay and motor deficits with activation of inflammatory pathways in monocytes [scRNA-seq]

GSE274183 Mus musculus (mouse) Single-cell RNA-seq 24 samples Submitted 2024/10/02 Platform GPL30172

At a glance

Single-cell RNA-seq · mouse · 24 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Mus musculus (mouse)
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: A Novel Non-Invasive Murine Model of Neonatal Hypoxic-Ischemic Encephalopathy Demonstrates Developmental Delay and Motor Deficits with Activation of Inflammatory Pathways in MonocytesCells · 2024

Summary (written by the submitters)

Neonatal hypoxic ischemic encephalopathy (HIE) occurs in 1.5 per 1000 live births, leaving affected children with long-term motor and cognitive deficits. Few animal models of HIE incorporate maternal immune activation (MIA) despite the significant risk MIA poses to HIE incidence and diagnosis. Our non-invasive model of HIE pairs late gestation MIA with postnatal hypoxia.

Read the full summary ↓

HIE pups exhibited a trend toward smaller overall brain size and delays in the ontogeny of several developmental milestones. In adulthood, HIE animals had reduced strength and gait deficits, but no difference in speed. Surprisingly, HIE animals performed better on the rotarod, an assessment of motor coordination. There was significant upregulation of inflammatory genes in microglia 24 hours after hypoxia, which were largely downregulated one week later. Single cell RNAseq revealed upregulation of epigenetic machinery in macrophages invading the brain following HIE. These results support a two-hit noninvasive model pairing MIA and hypoxia as a model for HIE in humans. This model results in a mild phenotype compared to established HIE models; however, HIE is a clinically heterogeneous injury resulting in a variety of outcomes in humans. The pathways identified in our model of HIE may yield novel targets for therapy for neonates with HIE.

Published in

A Novel Non-Invasive Murine Model of Neonatal Hypoxic-Ischemic Encephalopathy Demonstrates Developmental Delay and Motor Deficits with Activation of Inflammatory Pathways in Monocytes

Lemanski EA, Collins BA, Ebenezer AT et al. · Cells 2024 · PMID 39329733 · doi:10.3390/cells13181551

This dataset

Open GSE274183 in finder → Find more mouse 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 GSE274183_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1145365 and SRA study SRP524870. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39329733) ↗

Study design

6 conditions, mostly with about 4 replicates each

44 ×4 54 ×4 56 ×4 59 ×4 60 ×4 63 ×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

GSM8444753 44-1 44
GSM8444754 44-9 44
GSM8444755 44-2 44
GSM8444756 44-6 44
GSM8444757 54-2 54
GSM8444758 54-3 54
GSM8444759 54-5 54
GSM8444760 54-6 54
GSM8444761 56-1 56
GSM8444762 56-2 56
GSM8444763 56-3 56
GSM8444764 56-4 56
GSM8444765 59-1 59
GSM8444766 59-2 59
GSM8444767 59-9 59
GSM8444768 59-10 59
GSM8444769 60-4 60
GSM8444770 60-5 60
GSM8444771 60-6 60
GSM8444772 60-7 60
GSM8444773 63-1 63
GSM8444774 63-2 63
GSM8444775 63-3 63
GSM8444776 63-4 63

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