GEO series

Se Deficiency Exacerbates Hyperoxia-Induced Lung Injury in Newborn C3H/HeN Mice

GSE255744 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2024/05/01 Platform GPL30172

At a glance

RNA-seq (gene expression) · mouse · 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: Mus musculus (mouse)
Samples: 24 samples: 8 conditions, mostly in triplicateGroups 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: Selenium Deficiency Exacerbates Hyperoxia-Induced Lung Injury in Newborn C3H/HeN MiceAntioxidants (Basel, Switzerland) · 2024

Summary (written by the submitters)

Extremely preterm infants are often treated with supraphysiological oxygen which contributes to the development of bronchopulmonary dysplasia (BPD). These same infants exhibit compromised antioxidant capacities due in part to selenium (Se) deficiency. The present study was designed to develop a perinatal Se deficiency mouse model, identify the effects of newborn hyperoxia exposure, and explore alternative pathways affected by Se deficiency (SeD) that would contribute to impaired lung development.

Read the full summary ↓

Se deficient breeding pairs were generated, once pups were born, they were exposed to room air or 85% O2 for 14 d. Survival, antioxidant and Nrf2-regulated protein expression, and RNA seq analyses were performed. Greater than 40% mortality was observed in Se deficient (SeD), hyperoxia exposed pups. Surviving SeD pups had greater lung growth deficits than Se sufficient (SeS) pups exposed to hyperoxia. Gpx2 and 4 protein and Gpx activity were significantly decreased in SeD pups. Nrf2-regulated proteins, NQO1 and Gclc were increased in the setting of Se deficiency and hyperoxia exposure. RNA seq revealed significant decreases in the Wnt/-catenin and Notch pathways. Se is a biologically relevant modulator of perinatal lung development and antioxidant responses, especially in the context of hyperoxia exposure. RNA seq implicates pathways essential for normal lung development are dysregulated by Se deficiency.

Published in

Selenium Deficiency Exacerbates Hyperoxia-Induced Lung Injury in Newborn C3H/HeN Mice

Bailey-Downs LC, Sherlock LG, Crossley MN et al. · Antioxidants (Basel, Switzerland) 2024 · PMID 38671839 · doi:10.3390/antiox13040391

This dataset

Open GSE255744 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 GSE255744_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 PRJNA1076259 and SRA study SRP489636. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38671839) ↗

Study design

8 conditions, mostly in triplicate

SeS, hyperoxia, PN1, ×3 SeD, Room Air, PN1, ×3 SeD, hyperoxia, PN1, ×3 SeS, Room Air, PN1, ×3 SeS, hyperoxia, PN3, ×3 SeS, Room Air, PN3, ×3 SeD, hyperoxia, PN3, ×3 SeD, Room Air, PN3, ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 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

GSM8078846 SeS, hyperoxia, PN1, Replicate 1 SeS, hyperoxia, PN1,
GSM8078847 SeS, hyperoxia, PN1, Replicate 2 SeS, hyperoxia, PN1,
GSM8078848 SeD, Room Air, PN1, Replicate 1 SeD, Room Air, PN1,
GSM8078849 SeD, hyperoxia, PN1, Replicate 1 SeD, hyperoxia, PN1,
GSM8078850 SeS, hyperoxia, PN1, Replicate 3 SeS, hyperoxia, PN1,
GSM8078851 SeD, hyperoxia, PN1, Replicate 2 SeD, hyperoxia, PN1,
GSM8078852 SeS, Room Air, PN1, Replicate 1 SeS, Room Air, PN1,
GSM8078853 SeD, hyperoxia, PN1, Replicate 3 SeD, hyperoxia, PN1,
GSM8078854 SeS, Room Air, PN1, Replicate 2 SeS, Room Air, PN1,
GSM8078855 SeS, Room Air, PN1, Replicate 3 SeS, Room Air, PN1,
GSM8078856 SeS, hyperoxia, PN3, Replicate 1 SeS, hyperoxia, PN3,
GSM8078857 SeD, Room Air, PN1, Replicate 2 SeD, Room Air, PN1,
GSM8078858 SeS, hyperoxia, PN3, Replicate 2 SeS, hyperoxia, PN3,
GSM8078859 SeD, Room Air, PN1, Replicate 3 SeD, Room Air, PN1,
GSM8078860 SeS, hyperoxia, PN3, Replicate 3 SeS, hyperoxia, PN3,
GSM8078861 SeS, Room Air, PN3, Replicate 1 SeS, Room Air, PN3,
GSM8078862 SeS, Room Air, PN3, Replicate 2 SeS, Room Air, PN3,
GSM8078863 SeS, Room Air, PN3, Replicate 3 SeS, Room Air, PN3,
GSM8078864 SeD, hyperoxia, PN3, Replicate 1 SeD, hyperoxia, PN3,
GSM8078865 SeD, hyperoxia, PN3, Replicate 2 SeD, hyperoxia, PN3,
GSM8078866 SeD, Room Air, PN3, Replicate 1 SeD, Room Air, PN3,
GSM8078867 SeD, hyperoxia, PN3, Replicate 3 SeD, hyperoxia, PN3,
GSM8078868 SeD, Room Air, PN3, Replicate 2 SeD, Room Air, PN3,
GSM8078869 SeD, Room Air, PN3, Replicate 3 SeD, Room Air, PN3,

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