Mapping spatially resolved transcriptomes in human and mouse pulmonary fibrosis
RNA-seq (gene expression) · mouse · 24 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
- 24 samples: 3 × d7, ctrl, vs 3 × d7, bleo, vs 3 × d21, ctrl, vs 3 × d21, bleo,Groups 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
- Mapping spatially resolved transcriptomes in human and mouse pulmonary fibrosisNature genetics · 2024
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 GSE267904_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: 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 PRJNA1113613 and SRA study SRP508758. 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 24 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.
- GSM8281384 d7, ctrl, 1 d7, ctrl,
- GSM8281385 d7, ctrl, 2 d7, ctrl,
- GSM8281386 d7, ctrl, 3 d7, ctrl,
- GSM8281387 d7, bleo, 1 d7, bleo,
- GSM8281388 d7, bleo, 2 d7, bleo,
- GSM8281389 d7, bleo, 3 d7, bleo,
- GSM8281390 d7, bleo, 4a
- GSM8281391 d7, bleo, 5a
- GSM8281392 d7, bleo, 6a
- GSM8281393 d7, bleo, 4b
- GSM8281394 d7, bleo, 5b
- GSM8281395 d7, bleo, 6b
- GSM8281396 d21, ctrl, 1 d21, ctrl,
- GSM8281397 d21, ctrl, 2 d21, ctrl,
- GSM8281398 d21, ctrl, 3 d21, ctrl,
- GSM8281399 d21, bleo, 1 d21, bleo,
- GSM8281400 d21, bleo, 2 d21, bleo,
- GSM8281401 d21, bleo, 3 d21, bleo,
- GSM8281402 d21, bleo, 4a
- GSM8281403 d21, bleo, 5a
- GSM8281404 d21, bleo, 6a
- GSM8281405 d21, bleo, 4b
- GSM8281406 d21, bleo, 5b
- GSM8281407 d21, bleo, 6b
- GSE301216 Distinct lung functional, histological and cell senescence signatures in the single vs repetitive bleomycin mouse model of idiopathic pulmonary fibrosis 53 samples shares pulmonary, fibrosis
- GSE309471 Single-cell RNA sequencing of lung cells from bleomycin-induced and doxycycline-inducible TGF-β transgenic mouse models of pulmonary fibrosis 46 samples shares pulmonary, fibrosis
- GSE308578 Consistent lack of efficacy of nintedanib in a spirometry-confirmed and bleomycin-induced mouse model of idiopathic pulmonary fibrosis 43 samples shares pulmonary, fibrosis
- GSE289939 Gene expression profiling of mouse lung tissue in a bleomycin-induced pulmonary fibrosis model 15 samples shares pulmonary, fibrosis
- GSE295426 Targeting branched-chain amino acids alleviates pulmonary fibrosis [RNA-seq] 54 samples shares pulmonary, fibrosis
- GSE307419 Pulmonary fibroblast subsets demonstrate differentially enriched signaling pathways during fibrosis resolution and repair 26 samples shares pulmonary, fibrosis
- GSE337095 Remote ischemic conditioning mitigates diesel exhaust-induced pulmonary fibrosis by alleviating pulmonary inflammation and fibrogenesis 24 samples shares pulmonary, fibrosis
- GSE314582 Toll-Like-Receptor 5 Reduces Lung Dysbiosis and Protects Against Pulmonary Fibrosis 18 samples shares pulmonary, fibrosis
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.