Profibrotic monocyte-derived alveolar macrophages as a biomarker and therapeutic target in systemic sclerosis-associated interstitial lung disease [Northwestern]
Single-cell RNA-seq · human · 15 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
- Organism
- Homo sapiens (human)
- Samples
- 15 samples: 8 × BAL, SSc vs 5 × BAL, Healthy Voluntee vs 2 × BAL, SSc 02Groups 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
- Profibrotic monocyte-derived alveolar macrophages as a biomarker and therapeutic target in systemic sclerosis-associated interstitial lung diseasebioRxiv : the preprint server for biology · 2025
Read the full summary ↓
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE303859_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1297777. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 15 samples.
How we read this: 3 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.
- GSM9137049 BAL, Healthy Volunteer 9 BAL, Healthy Voluntee
- GSM9137050 BAL, Healthy Volunteer 10 BAL, Healthy Voluntee
- GSM9137051 BAL, Healthy Volunteer 11 BAL, Healthy Voluntee
- GSM9137052 BAL, Healthy Volunteer 12 BAL, Healthy Voluntee
- GSM9137053 BAL, Healthy Volunteer 13 BAL, Healthy Voluntee
- GSM9137054 BAL, SSc 01 BAL, SSc
- GSM9137055 BAL, SSc 02-1 BAL, SSc 02
- GSM9137056 BAL, SSc 03 BAL, SSc
- GSM9137057 BAL, SSc 02-2 BAL, SSc 02
- GSM9137058 BAL, SSc 04 BAL, SSc
- GSM9137059 BAL, SSc 05 BAL, SSc
- GSM9137060 BAL, SSc 06 BAL, SSc
- GSM9137061 BAL, SSc 07 BAL, SSc
- GSM9137062 BAL, SSc 08 BAL, SSc
- GSM9137063 BAL, SSc 09 BAL, SSc
- GSE303858 Profibrotic monocyte-derived alveolar macrophages as a biomarker and therapeutic target in systemic sclerosis-associated interstitial lung disease [Duke] 8 samples shares sclerosis-associated, monocyte-derived, interstitial, profibrotic, macrophages, therapeutic, biomarker
- GSE232628 Expansion of profibrotic monocyte-derived alveolar macrophages in patients with persistent respiratory symptoms and radiographic abnormalities after COVID-19 46 samples shares monocyte-derived, profibrotic, macrophages
- GSE232627 Expansion of profibrotic monocyte-derived alveolar macrophages in patients with persistent respiratory symptoms and radiographic abnormalities after COVID-19 [PASC] 30 samples shares monocyte-derived, profibrotic, macrophages
- GSE232616 Expansion of profibrotic monocyte-derived alveolar macrophages in patients with persistent respiratory symptoms and radiographic abnormalities after COVID-19 [BAL] 8 samples shares monocyte-derived, profibrotic, macrophages
- GSE232623 Expansion of profibrotic monocyte-derived alveolar macrophages in patients with persistent respiratory symptoms and radiographic abnormalities after COVID-19 [NEP] 8 samples shares monocyte-derived, profibrotic, macrophages
- GSE236156 Mycobacterium tuberculosis induced interferon pathways distinguish responses of Human Alveolar Macrophages from Monocyte-Derived Macrophages 55 samples shares monocyte-derived, macrophages
- GSE335752 Characterization of human M2-like (TGFbeta/IL10) vs M0 monocyte-derived macrophages 36 samples shares monocyte-derived, macrophages
- GSE316027 β-hydroxybutyrate-driven histone lysine β-hydroxybutyrylation promotes the immunostimulatory activity of monocyte-derived macrophages in rectal cancer 32 samples shares monocyte-derived, macrophages
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.