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AS01-adjuvanted vaccine promotes functional and epigenetic modifications in monocytes [scRNA-seq]

GSE244793 Homo sapiens (human) Single-cell RNA-seq 31 samples Submitted 2024/07/31 Platform GPL24676
At a glance

Single-cell RNA-seq · human · 31 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Homo sapiens (human)
Samples
31 samples: 5 conditions, mostly with about 7 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
Functional and epigenetic changes in monocytes from adults immunized with an AS01-adjuvanted vaccineScience translational medicine · 2024
Summary (written by the submitters)
HBS/AS01 adjuvanted vaccine induces changes in the chromatin structure in monocytes impacting their gene expression profiles, an effect that lasts until 6 months post vaccination
Published in
Functional and epigenetic changes in monocytes from adults immunized with an AS01-adjuvanted vaccine
Bechtold V, Smolen KK, Burny W et al. · Science translational medicine 2024 · PMID 39083587 · doi:10.1126/scitranslmed.adl3381
This dataset
Open GSE244793 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 GSE244793_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: 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 PRJNA1024905. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39083587) ↗
Study design
5 conditions, mostly with about 7 replicates each
GEX, D0, S ×7 GEX, D180, S ×7 GEX, D32, S ×7 GEX, D44, S ×7 GEX, D60, S ×3

Supports a between-group comparison across 31 samples.

How we read this: 5 replicated groups read from 31 sample titles; they account for 31 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

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