GEO series

scRNAseq Data Analysis Code Muscle Inflammation is Regulated by NF-kB From Multiple Cells to Control Distinct States of Wasting in Cancer Cachexia

GSE248800 Homo sapiens (human) Single-cell RNA-seq 17 samples Submitted 2025/01/15 Platform GPL24676Platform GPL24247

At a glance

Single-cell RNA-seq · human · 17 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Homo sapiens (human)
Samples: 17 samples: 14 distinct titles, 3 of them repeatedGroups 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)

Although cancer cachexia is classically characterized as a systemic inflammatory disorder, emerging evidence indicates that weight loss also associates with local tissue inflammation. We queried the regulation of this inflammation and its causality to cachexia by exploring skeletal muscle, whose atrophy strongly associates with poor outcome.

Read the full summary ↓

Using multiple mouse models and patient samples, we show that cachectic muscle is marked by enhanced innate immunity. NF-kB activity in multiple cells, including satellite cells, myofibers, and fibro-adipogenic progenitors, promotes macrophage expansion derived equally from infiltrating monocytes and resident tissue. Moreover, NF-kB activated cells and macrophages undergo crosstalk: whereas NF-kB+ cells recruit macrophages to inhibit regeneration and promote atrophy, while interestingly also protecting myofibers, macrophages stimulate NF-kB+ cells in a feed forward loop to sustain inflammation. Together, we propose that NF-kB functions in multiple cells in the muscle microenvironment to stimulate macrophage inflammation that both promotes and protects against muscle wasting in cancer.

This dataset

Open GSE248800 in finder → Find more 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 GSE248800_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1046037 and SRA study SRP474657. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

14 distinct titles, 3 of them repeated

C26neg_s ×2 posControl_s ×2 C26pos_s ×2

How we read this: Read from 17 sample titles: 14 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

GSM7920254 Neg_WS_PDAC
GSM7920255 Pos_WS_PDAC
GSM7920256 Neg_Control
GSM7920257 Pos_Control
GSM7920258 Neg_C_PDAC
GSM7920259 Pos_C_PDAC
GSM7920260 Ctrl_Neg
GSM7920261 Kpp_Neg
GSM7920262 Ctrl_Pos
GSM7920263 Kpp_Pos
GSM7920264 negControl_s1
GSM7920265 C26neg_s1
GSM7920266 posControl_s1
GSM7920267 C26pos_s1
GSM7920268 posControl_s2
GSM7920269 C26pos_s2
GSM7920270 C26neg_s2

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