← BioTransfer GEO Dataset Finder
GEO series

Brugia malayi filarial helminth-derived extracellular vesicles suppress antigen presenting cell functions and antigen-specific CD4+ T cell responses

GSE263690 Homo sapiens (human) RNA-seq (gene expression) 20 samples Submitted 2024/08/20 Platform GPL18573
At a glance

RNA-seq (gene expression) · human · 20 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
20 samples: 5 conditions, mostly with about 4 replicates eachGroups 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
Brugia malayi filarial helminth-derived extracellular vesicles suppress antigen presenting cell function and antigen-specific CD4+ T cell responsesFrontiers in immunology · 2024
Summary (written by the submitters)
Live microfilariae (Mf) and mf-derived extracellular vesicles (EVs) have been shown to modulate human antigen presenting cell (APC) function, most notably by suppressing the induction of IL-12 (and other pro-inflammatory cytokines) following activation with LPS and interferon-gamma. To explore further how EVs alter human APC function, we studied the effect of mf and EVs on human elutriated monocyte-derived DCs following exposure to Mf, Mf-derived excretrory/secretory (E/S) products, E/S depleted of EVs through ultracentrifugation and purified EVs using RNAseq analysis.
Read the full summary ↓
In our analyses of the data for the DC, using a false discovery rate (FDR)<0.05, EV-exposed DCs had induced the expression of 212 differentially expressed genes (DEGs) when compared to unexposed DC and 157 when compared to ES-depleted EVs. These genes were enriched in GO biological processes associated with neutrophil degranulation and 15 DEGs associated with KEGG Lysosome pathways. IPA analysis point to immune dysregulation.
Published in
Brugia malayi filarial helminth-derived extracellular vesicles suppress antigen presenting cell function and antigen-specific CD4+ T cell responses
Sanku G, Ricciardi A, Redekar NR et al. · Frontiers in immunology 2024 · PMID 39434874 · doi:10.3389/fimmu.2024.1436818
This dataset
Open GSE263690 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 GSE263690_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 PRJNA1098733 and SRA study SRP500813. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39434874) ↗
Study design
5 conditions, mostly with about 4 replicates each
Mono-derived DC, EV depleted E/S, ×4 Mono-derived DC, Mf live, ×4 Mono-derived DC, Mf-derived excretory/secreto… ×4 Mono-derived DC, Mf-derived extracellular ves… ×4 Mono-derived DC, unconditioned, ×4

Supports a between-group comparison across 20 samples.

How we read this: 5 replicated groups read from 20 sample titles; they account for 20 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
Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

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.