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Ketogenicdiet versus standard high-carbohydrate nutrition in sepsis: a randomized controlled trial

GSE240861 Homo sapiens (human) RNA-seq (gene expression) 100 samples Submitted 2024/06/13 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 100 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
100 samples: 49 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
An open-label, randomized controlled trial to assess a ketogenic diet in critically ill patients with sepsisScience translational medicine · 2024
Summary (written by the submitters)
Sepsis patients suffer from severe metabolic and immunologic dysfunction that may be amplified by standard nutritional approaches relying primarily on carbohydrates. We here hypothesize that a ketogenic diet improves sepsis treatment. We conducted a monocentric open-labeled randomized controlled trial enrolling 40 adult sepsis patients.
Read the full summary ↓
Patients were randomly assigned to either ketogenic diet (KD) or standard high-carbohydrate nutrition for 14 days and followed up until day 30. The primary outcome measure was β-hydroxybutyrate (BHB) serum concentration on day 14. We assessed feasibility and safety of KD, as well as diet-associated clinical and immunological changes. The respective nutrition protocols were successfully applied, dropouts did not occur. Regression analysis revealed a greater increase in BHB concentrations from baseline to day 14 in KD patients compared to controls. Metabolic side effects were not observed under ketogenic diet. Ventilation-free, vasopressor-free, dialysis-free and ICU-free days significantly increased in patients under ketogenic diet. Transcriptome profiling of both CD4+ and CD8+ T cells at day 14 revealed substantial differential regulation of gene expression in the KD vs. the control group indicating a reduced T-cell activation and a shift towards a more regulated immunity.
Published in
An open-label, randomized controlled trial to assess a ketogenic diet in critically ill patients with sepsis
Rahmel T, Effinger D, Bracht T et al. · Science translational medicine 2024 · PMID 38985853 · doi:10.1126/scitranslmed.adn9285
This dataset
Open GSE240861 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 GSE240861_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 PRJNA1005592 and SRA study SRP455194. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38985853) ↗
Study design
49 conditions, mostly in duplicate
CD4_1 ×2 CD4_3 ×2 CD4_4 ×2 CD4_5 ×2 CD4_8 ×2 CD4_10 ×2 CD4_12 ×2 CD4_13 ×2 +43 more

Supports a between-group comparison across 98 samples.

How we read this: 49 replicated groups read from 100 sample titles; they account for 98 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

+ 60 more — browse all 100 samples with per-sample file links →

Datasets on a similar topic

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