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Extramedullary hematopoiesis and immune training drive systemic inflammation and associated organ damage in Systemic Lupus Erythematosus

GSE218780 Mus musculus (mouse) DNA methylation 22 samples Submitted 2024/03/20 Platform GPL17021Platform GPL19057
At a glance

DNA methylation · mouse · 22 samples

What it is
DNA methylationChemical marks on DNA that help switch genes on or off.
Organism
Mus musculus (mouse)
Samples
22 samples: 6 conditions, mostly in triplicateGroups 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
Enhanced medullary and extramedullary granulopoiesis sustain the inflammatory response in lupus nephritisLupus science & medicine · 2024
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
Enhanced medullary and extramedullary granulopoiesis sustain the inflammatory response in lupus nephritis
Zervopoulou E, Grigoriou M, Doumas SA et al. · Lupus science & medicine 2024 · PMID 38471723 · doi:10.1136/lupus-2023-001110
This dataset
Open GSE218780 in finder → Find more mouse 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 GSE218780_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 beta-value tables or raw IDAT files among the supplementary files.

Also filed as BioProject PRJNA905434 and SRA study SRP409818. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38471723) ↗
Study design
6 conditions, mostly in triplicate
Bone Marrow-derived LSK cells from Predisease… ×6 Bone Marrow-derived LSK cells from Lupus mice ×4 PBS-treated LSK cells from Bone Marrow ×3 b-glucan-treated LSK cells from Bone Marrow ×3 PBS-treated LSK cells from Spleen ×3 b-glucan-treated LSK cells from Spleen ×3

Supports a between-group comparison across 22 samples.

How we read this: 6 replicated groups read from 22 sample titles; they account for 22 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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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.