GEO series

Sympathetic neuron-associated macrophages contribute to obesity by importing and metabolizing norepinephrine

GSE103847 Mus musculus (mouse) RNA-seq (gene expression) 15 samples Submitted 2017/10/09 Platform GPL19057

At a glance

RNA-seq (gene expression) · mouse · 15 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: 15 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.

Summary (written by the submitters)

The cellular mechanism(s) linking macrophages to norepinephrine (NE)-mediated regulation of thermogenesis has been a topic of debate. Here, we identify sympathetic neuron-associated macrophages (SAMs) as a population of macrophages that mediate clearance of NE via expression of Slc6a2, an NE transporter, and monoamine oxidase A (MAOa), a degradation enzyme.

Read the full summary ↓

Optogenetic activation of the SNS upregulates NE uptake by SAMs and shifts the SAM profile to a more pro-inflammatory state. NE uptake by SAMs is prevented by genetic depletion of Slc6a2 or inhibition of the transporter. We also found that obesity increases SAM content in the SNS. In two mouse models of obesity, genetic ablation of Slc6a2 in SAMs increases brown adipose tissue (BAT) content, causes browning of white fat, increases thermogenesis and leads to significant and sustained weight loss. We further show that this pathway is conserved as human sympathetic ganglia also contain SAMs and the analogous molecular machinery for NE clearance, thus constituting a potential target for obesity treatment.

This dataset

Open GSE103847 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 GSE103847_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 PRJNA407286 and SRA study SRP117660. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 29035364) ↗

Study design

6 conditions, mostly in triplicate

Microglia_ND ×3 SAM_ganglia_ND ×3 SpM_ND ×3 SAM_fibers_ND ×2 sATM_ND ×2 vATM_ND ×2

Supports a between-group comparison across 15 samples.

How we read this: 6 replicated groups read from 15 sample titles; they account for 15 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

GSM2784578 Microglia_ND_rep1 Microglia_ND
GSM2784579 Microglia_ND_rep2 Microglia_ND
GSM2784580 Microglia_ND_rep3 Microglia_ND
GSM2784581 SAM_fibers_ND_rep1 SAM_fibers_ND
GSM2784582 SAM_fibers_ND_rep2 SAM_fibers_ND
GSM2784583 SAM_ganglia_ND_rep1 SAM_ganglia_ND
GSM2784584 SAM_ganglia_ND_rep2 SAM_ganglia_ND
GSM2784585 SAM_ganglia_ND_rep3 SAM_ganglia_ND
GSM2784586 sATM_ND_rep1 sATM_ND
GSM2784587 sATM_ND_rep2 sATM_ND
GSM2784588 SpM_ND_rep1 SpM_ND
GSM2784589 SpM_ND_rep2 SpM_ND
GSM2784590 SpM_ND_rep3 SpM_ND
GSM2784591 vATM_ND_rep1 vATM_ND
GSM2784592 vATM_ND_rep2 vATM_ND

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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.