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Single cell RNAseq analysis of PBMCs isolated from healthy adults subjeccted to sleep restriction

GSE275071 Homo sapiens (human) Single-cell RNA-seq 32 samples Submitted 2024/10/30 Platform GPL34281
At a glance

Single-cell RNA-seq · human · 32 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
32 samples: 8 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
Myocardial infarction augments sleep to limit cardiac inflammation and damageNature · 2024
Summary (written by the submitters)
How sleep influences the transcriptional programing of blood leukocytes in humans remains incompletely undertstood. Volunteers with adequate sleep participated in a 6 week cross-over design trial. During the habitual sleep (HS) phase, participants did not alter their sleep and slept adequately. During the sleep restriction phase (SR), participants restricted their sleep by ∼1.5 hours per night. PBMCs from 8 individuals (4 HS and 4 SR) were collected subjected to scRNAseq.
Published in
Myocardial infarction augments sleep to limit cardiac inflammation and damage
Huynh P, Hoffmann JD, Gerhardt T et al. · Nature 2024 · PMID 39478215 · doi:10.1038/s41586-024-08100-w
This dataset
Open GSE275071 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 GSE275071_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 PRJNA1149055 and SRA study SRP526919. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39478215) ↗
Study design
8 conditions, mostly with about 4 replicates each
PBMC, habitual sleep, participant 1, GEM well/ ×4 PBMC, habitual sleep, participant 2, GEM well/ ×4 PBMC, habitual sleep, participant 3, GEM well/ ×4 PBMC, habitual sleep, participant 4, GEM well/ ×4 PBMC, sleep restriction, participant 5, GEM w… ×4 PBMC, sleep restriction, participant 6, GEM w… ×4 PBMC, sleep restriction, participant 7, GEM w… ×4 PBMC, sleep restriction, participant 8, GEM w… ×4

Supports a between-group comparison across 32 samples.

How we read this: 8 replicated groups read from 32 sample titles; they account for 32 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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