Spatially resolved atlas of IPF fibroblastic foci identifies that PAK2 kinase activation is involved in fibrogenesis
Single-cell RNA-seq · human · 12 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
- 12 samples: 4 × Visium_JKPF3 vs 3 × Visium_JKPF2 vs 3 × scRNA_JKPF vs 2 × Visium_JKPF1Groups 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
- Integrated spatial and single-cell transcriptomics reveal PAK kinase as a therapeutic target in fibroblastic foci and dense fibrosis of idiopathic pulmonary fibrosisThe European respiratory journal · 2025
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 GSE285246_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 PRJNA1202105 and SRA study SRP553467. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM8699165 Visium_JKPF1_1 Visium_JKPF1
- GSM8699166 Visium_JKPF1_2 Visium_JKPF1
- GSM8699167 Visium_JKPF2_1 Visium_JKPF2
- GSM8699168 Visium_JKPF2_2 Visium_JKPF2
- GSM8699169 Visium_JKPF2_3 Visium_JKPF2
- GSM8699170 Visium_JKPF3_1 Visium_JKPF3
- GSM8699171 Visium_JKPF3_2 Visium_JKPF3
- GSM8699172 Visium_JKPF3_3 Visium_JKPF3
- GSM8699173 Visium_JKPF3_5 Visium_JKPF3
- GSM8699174 scRNA_JKPF1 scRNA_JKPF
- GSM8699175 scRNA_JKPF2 scRNA_JKPF
- GSM8699176 scRNA_JKPF3 scRNA_JKPF
- GSE15197 RNA Expression Profiling of Lung Tissue Identifies Mutually Distinct Molecular Signatures in PAH and PH Secondary to IPF 39 samples shares ipf, identifies
- GSE217046 Glutamine deficiency drives transforming growth factor-β signaling activation that gives rise to myofibroblastic carcinoma-associated fibroblasts 12 samples shares fibroblastic, activation
- GSE267521 The MUC5B IPF risk variant promotes a distal airway secretory phenotype and loss of alveolar markers 310 samples shares ipf
- GSE286182 Single Nuclear RNAseq and MultiOme of IPF and Control Lung Tissue 75 samples shares ipf
- GSE159354 Single-cell RNA-seq of sort human lung explants from IPF and SSc-ILD patients 48 samples shares ipf
- GSE53845 40 IPF patients and 8 healthy controls 48 samples shares ipf
- GSE301181 Identification of IPF Specific Genes Expressed by Lung Tissue - Derived Fibroblasts Using Next Generation Sequencing 43 samples shares ipf
- GSE92592 mRNA Sequencing of Ideopathic Pulmonary Fibrosis (IPF) and Control Samples from the Lung Tissue Research Consortium (LTRC) 39 samples shares ipf
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.