GEO series

Comparison of sorted TRM populations and TRM-like cells in vitro

GSE196376 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2026/01/22 Platform GPL30172

At a glance

RNA-seq (gene expression) · mouse · 24 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: Mus musculus (mouse)
Samples: 24 samples
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: An improved organotypic cell culture system to study tissue-resident macrophages ex vivoCell reports methods · 2022

Summary (written by the submitters)

Tissue-resident macrophages (TRM) perform organ-specific functions that are dependent on factors such as hematopoietic origin, local environment and biological influences. A diverse range of in vitro culture systems have been developed to decipher TRM functions, including bone marrow-derived macrophages (BMDM), induced pluripotent stem cells (iPSC) or immortalized cell lines.

Read the full summary ↓

However, despite the usefulness of such systems, there are notable limitations. Attempts to culture primary macrophages often require purification of cells, lack a high cell yield and consistent phenotype. Here, we aimed to address these practical limitations by establishing a new organotypic primary cell culture protocol. We obtained long-term monocultures of macrophages derived from distinct organs without FACS or MACS purification using specific growth factors and tissue normoxic conditions that largely conserved a TRM-like identity in vitro. Thus, this new organotypic system offers an ideal screening platform for primary macrophages from different organs which can be used for a wide range of assays and read-outs.

Published in

An improved organotypic cell culture system to study tissue-resident macrophages ex vivo

Aktories P, Petry P, Glatz P et al. · Cell reports methods 2022 · PMID 36046625 · doi:10.1016/j.crmeth.2022.100260

This dataset

Open GSE196376 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 GSE196376_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 PRJNA804542 and SRA study SRP358947. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 36046625) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 24 more — browse all 24 samples with per-sample file links →

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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.