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German cockroach subcutaneous immunotherapy: Impact on nasal responses and allergen-specific immunity among urban children with asthma

GSE250580 Homo sapiens (human) RNA-seq (gene expression) 266 samples Submitted 2024/12/18 Platform GPL30173Platform GPL16791
At a glance

RNA-seq (gene expression) · human · 266 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
266 samples: 102 conditions, mostly in duplicateGroups 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 pediatric randomized, controlled trial of German cockroach subcutaneous immunotherapyThe Journal of allergy and clinical immunology · 2024
Summary (written by the submitters)
Background: Cockroach allergy contributes to morbidity among urban children with asthma. Few trials address the effect of subcutaneous immunotherapy (SCIT) with cockroach allergen among these at-risk children.Objective: To determine if nasal allergen challenge (NAC) responses to cockroach allergen would improve following one year of SCIT.Methods: Urban children with asthma, cockroach-sensitized (skin prick test [SPT] and serum specific IgE) and reactive on NAC, participated in a yearlong randomized double-blind placebo-controlled SCIT trial using German cockroach extract.
Read the full summary ↓
The primary endpoint was the change in mean total nasal symptoms scores (TNSS) during NAC after 12 months of SCIT. Changes in nasal transcriptomic responses during NAC, SPT wheal size, serum allergen-specific antibody production and T-cell responses to cockroach allergen were assessed.Results: Changes in mean NAC TNSS did not differ between SCIT-assigned (n=28) versus placebo-assigned (n=29) participants (p=0.63). Nasal transcriptomic responses correlated with TNSS, but a treatment effect was not observed. Cockroach sIgE decreased to a similar extent in both groups, while decreased cockroach SPT wheal size was greater among SCIT participants (p=0.04). A 200-fold increase in cockroach sIgG4 was observed among subjects receiving SCIT (p<0.001) but was unchanged in the placebo group. T-cell interleukin-4 responses following cockroach allergen stimulation decreased to a greater extent among SCIT versus placebo (p=0.002), while no effect was observed for interleukin-10 or interferon-gamma.Conclusion: A year of SCIT failed to alter NAC TNSS and nasal transcriptome responses to cockroach allergen challenge despite systemic effects on allergen-specific skin tests, induction of serum sIgG4 production and down-modulation of allergen stimulated T-cell responses.
Published in
A pediatric randomized, controlled trial of German cockroach subcutaneous immunotherapy
Zoratti E, Wood R, Pomés A et al. · The Journal of allergy and clinical immunology 2024 · PMID 38718950 · doi:10.1016/j.jaci.2024.04.022
This dataset
Open GSE250580 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 GSE250580_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 PRJNA1054571 and SRA study SRP478951. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38718950) ↗
Study design
102 conditions, mostly in duplicate
28-09-0001-4_pre ×2 28-09-0001-4_post ×2 28-09-0002-0_pre ×2 28-09-0002-0_post ×2 28-09-0004-2_pre ×2 28-09-0004-2_post ×2 28-07-0001-2_post ×2 28-07-0006-8_post ×2 +156 more

Supports a between-group comparison across 204 samples.

How we read this: 102 replicated groups read from 266 sample titles; they account for 204 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

+ 226 more — browse all 266 samples with per-sample file links →

Datasets on a similar topic

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