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Cardiopulmonary bypass activates classical monocytes via shear-mediated activation of Store-Operated Calcium Entry

GSE262146 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 48 samples Submitted 2025/03/19 Platform GPL24676
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 48 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Homo sapiens (human)
Samples
48 samples: 48 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
A shear stress-responsive pathway in monocytes drives cardiopulmonary bypass-induced inflammation via spectrin/RAF1/store-operated calcium entryCell reports · 2026
Summary (written by the submitters)
Exposure to cardiopulmonary bypass (CPB) during cardiac surgery results in a significant inflammatory response that contributes to morbidity and mortality, which is especially prominent in neonatal patients. The molecular and cellular mechanisms that underpin this inflammatory process remain poorly understood. To gain deeper insight, we performed snRNA and snATAC sequencing on peripheral blood mononuclear cells (PBMCs) isolated from neonatal CPB patients prior to start of CPB, at the end of CPB, as well as 8 and 24 hours after CPB.
Read the full summary ↓
The dramatic increase in the proportion of classic monocytes following bypass surgery indicates their essential role in inflammation associated with cardiopulmonary bypass (CPB). Immune dysregulation exhibited at activation of inflammatory genes in classical monocytes, as well as in other cell types, after CPB exposure. A series of in vitro experiments in non-adherent monocytic cells identified two novel genes SPTAN1 and RAF1 as effectors of hemodynamic stress. These two genes promoted STIM1 coupling to ORAI1 channel leading to calcium icon influx, thereby driving inflammation and cell death. snATAC-Seq revealed dynamically changing patterns of chromatin accessibility and transcription factors JUN and FOS binding motifs being highly enriched in classical monocytes after CPB exposure. Increased calcium in turn stimulates JUN binding to DNA, as suggested by CUT&RUN data derived from shear stressed non-adherent monocytic cells. Together, these data indicate that shear stress via a calcium dependent mechanism contributes to the CPB-associated activation of classic monocytes. These findings provide deeper insight not only in the pathogenesis of CPB-associated inflammation, but also have implications for the understanding of early stages of sterile inflammation and how non-adherent cells “sense” shear stress.
Published in
A shear stress-responsive pathway in monocytes drives cardiopulmonary bypass-induced inflammation via spectrin/RAF1/store-operated calcium entry
Li W, Tu LN, Hsieh L et al. · Cell reports 2026 · PMID 41579376 · doi:10.1016/j.celrep.2025.116903
This dataset
Open GSE262146 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 GSE262146_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1090473 and SRA study SRP497022. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41579376) ↗
Study design
48 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 48 sample titles: 48 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

+ 8 more — browse all 48 samples with per-sample file links →

Datasets on a similar topic

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