GEO series
Clinical and Immunological Outcomes after Randomized Trial of Baked Milk Oral Immunotherapy for Milk Allergy
GSE280063
Homo sapiens (human)
Single-cell RNA-seq
24 samples
Submitted 2025/01/13
Platform GPL24676
At a glance
Single-cell RNA-seq · human · 24 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
- Organism
- Homo sapiens (human)
- Samples
- 24 samples: 24 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.
- Paper
- Clinical and immunological outcomes after randomized trial of baked milk oral immunotherapy for milk allergyJCI insight · 2025
Summary (written by the submitters)
BACKGROUND. Cow’s milk allergy (CMA) is the most common food allergy in young children. Treatment with oral immunotherapy (OIT) has shown efficacy but also high rates of adverse reactions. We sought to determine if baked milk (BM) OIT could reduce adverse reactions while still inducing desensitization, and to identify immunological correlates of successful BMOIT.
Read the full summary ↓
METHODS. This phase II, randomized trial evaluated the safety and efficacy of BMOIT in children age 3-18 years. After the initial placebo-controlled first year of treatment, placebo-treated participants crossed over to active BMOIT for year two. Double-blind, placebo-controlled food challenges (DBPCFC) were conducted to BM after year one and to both BM and unheated milk (UM) after year two. IgG/IgE antibodies were measured along with cow’s milk (CM)-specific CD4 memory T cell populations, profiled using flow cytometry and scRNA-Seq. RESULTS. Twenty-one of 30 (70%) reached the primary endpoint of tolerating 4044mg of BM protein at month-24, and 11/30 tolerated ≥2000mg of UM. Dosing symptoms were common, but >98% were mild with no severe reactions. Immunological changes associated with desensitization included increased CM IgG4, CM+ FOXP3+ cells, and Tregs and corresponding decreases in CM IgE, CM+ Th2A cells, and CD154+ cells. T cell and antibody measurements were combined to build a model that predicted UM oral food challenge (OFC) outcomes. CONCLUSION. BMOIT was well tolerated and induced a substantial level of desensitization to baked and unheated milk. This desensitization corresponded to significant redistribution within antigen specific antibody and T cell compartments that provide novel insight into the mechanistic changes that occur with OIT treatment.
Published in
Dantzer JA, Lewis SA, Psoter KJ et al.
· JCI insight 2025
· PMID 39782691
· doi:10.1172/jci.insight.184301
This dataset
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.
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 GSE280063_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1176124. Searching any of these in the dataset finder brings you back here.
Study design
24 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 24 sample titles: 24 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
- GSM8586724 CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube1A
- GSM8586725 CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube1A
- GSM8586726 CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube1B
- GSM8586727 CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube1B
- GSM8586728 CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube2A
- GSM8586729 CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube2A
- GSM8586730 CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube2B
- GSM8586731 CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube2B
- GSM8586732 CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube3A
- GSM8586733 CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube3A
- GSM8586734 CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube3B
- GSM8586735 CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube3B
- GSM8586736 CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube4A
- GSM8586737 CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube4A
- GSM8586738 CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube4B
- GSM8586739 CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube4B
- GSM8586740 CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube5A
- GSM8586741 CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube5A
- GSM8586742 CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube5B
- GSM8586743 CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube5B
- GSM8586744 CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube6A
- GSM8586745 CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube6A
- GSM8586746 CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, hashtag, tube6B
- GSM8586747 CD4 memory T cells, cow milk allergic and non-allergic pediatric subjects, Gene expression, tube6B
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Share this dataset
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.