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Diminished pro-inflammatory characteristics in murine bone marrow derived macrophages with impaired thyroid hormone receptor alpha signaling

GSE317221 Mus musculus (mouse) RNA-seq (gene expression) 30 samples Submitted 2026/07/01 Platform GPL34290
At a glance

RNA-seq (gene expression) · mouse · 30 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
30 samples: 10 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.
Summary (written by the submitters)
Macrophages are versatile phagocytes of the innate immune system with functions ranging from pro-inflammatory to immunomodulatory. Macrophages are receptive to signals from thyroid hormones (THs). Here, we studied the role of the TH receptor (TR)α1 in macrophage function. Using wild type and transgenic mice with a mutation in the T3 binding domain of the TRα1 (TRα1PV), we generated bone marrow derived macrophages (BMDMs) and subsequently polarized them into pro-inflammatory or immunomodulatory phenotypes.
Read the full summary ↓
The phenotype and function of the unpolarized, pro-inflammatory and immunomodulatory TRα1PV BMDMs was compared to the respective wild type BMDMs. The pro-inflammatory TRα1PV BMDMs displayed decreased pro-inflammatory markers, while marker expression of unpolarized and immunomodulatory TRα1PV BMDMs was unaltered. Glycolysis, a characteristic of proinflammatory macrophages, was reduced in all three TRα1PV macrophage phenotypes. Moreover, RNA sequencing revealed different expression profiles and alterations of biological pathways, including immune functions in all TRα1PV BMDMs phenotypes. Altogether, we observed that the TRα1PV mutation results in phenotypical and functional different BMDMs, with most striking changes in the pro-inflammatory phenotype, underlining the significance of adequate T3-TRα1 signaling in pro-inflammatory macrophage responses.
This dataset
Open GSE317221 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 GSE317221_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 PRJNA1406286 and SRA study SRP665360. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
10 conditions, mostly in triplicate
BMDM, biol rep 1, WT, M ×3 BMDM, biol rep 1, TRα1PV, M ×3 BMDM, biol rep 2, WT, M ×3 BMDM, biol rep 2, TRα1PV, M ×3 BMDM, biol rep 3, WT, M ×3 BMDM, biol rep 3, TRα1PV, M ×3 BMDM, biol rep 4, WT, M ×3 BMDM, biol rep 4, TRα1PV, M ×3 +2 more

Supports a between-group comparison across 30 samples.

How we read this: 10 replicated groups read from 30 sample titles; they account for 30 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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