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Comprehensive transcriptomic analysis of immune-related genes in diabetic foot ulcers: New insights into mechanisms and therapeutic targets

GSE199939 Homo sapiens (human) RNA-seq (gene expression) 21 samples Submitted 2024/05/30 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 21 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
21 samples: 21 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
Comprehensive transcriptomic analysis of immune-related genes in diabetic foot ulcers: New insights into mechanisms and therapeutic targetsInternational immunopharmacology · 2024
Summary (written by the submitters)
We performed RNA-seq on tissue biopsies derived from patients with DFU and compared it to healthy controls who had similar foot surgery to identify the significant immune related differentially expressed genes between normal and DFU samples. Our results identified that there was a total of 8800 DEGs detected by RNA-seq data analysis, among which 2351 were upregulated and 6449 downregulated genes in DFU.
Read the full summary ↓
526 differential IRGs were obtained from intersection of DEGs and IRGs. These results suggest that a deregulated immune cells contribute to pathogenesis of DFUs.The purpose of this study was to identify the key biomarkers of the abnormally expressed genes and immune infiltration in the diabetic wound and to provide diagnostic and therapeutic targets for DFU.
Published in
Comprehensive transcriptomic analysis of immune-related genes in diabetic foot ulcers: New insights into mechanisms and therapeutic targets
Jiang N, Xu C, Xu Y et al. · International immunopharmacology 2024 · PMID 39079197 · doi:10.1016/j.intimp.2024.112638
This dataset
Open GSE199939 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 GSE199939_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 PRJNA822286 and SRA study SRP367217. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39079197) ↗
Study design
21 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 21 sample titles: 21 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
Datasets on a similar topic

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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.