Therapeutic Single-Cell Landscape: Methotrexate Exacerbates Interstitial Lung Disease by Compromising the Stemness of Alveolar Epithelial Cells under Systemic Inflammation
Single-cell RNA-seq · mouse · 16 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Mus musculus (mouse)
- Samples
- 16 samples: 16 samples, each with a distinct title — no replicated groupsGroups 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
- Therapeutic single-cell landscape: methotrexate exacerbates interstitial lung disease by compromising the stemness of alveolar epithelial cells under systemic inflammationEBioMedicine · 2024
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 GSE271209_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 PRJNA1130461 and SRA study SRP517264. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 8 samples read as cases, 8 as controls.
How we read this: Read from 16 sample titles: 16 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.
- GSM8371770 Positive CTL, replicate 1, snRNA-seq
- GSM8371771 Positive CTL, replicate 2, snRNA-seq
- GSM8371772 Positive CTL, replicate 3, snRNA-seq
- GSM8371773 Positive CTL, replicate 4, snRNA-seq
- GSM8371774 MTX-treated, replicate 1, snRNA-seq
- GSM8371775 MTX-treated, replicate 2, snRNA-seq
- GSM8371776 MTX-treated, replicate 3, snRNA-seq
- GSM8371777 MTX-treated, replicate 4, snRNA-seq
- GSM8371778 TNFi-treated, replicate 1, snRNA-seq
- GSM8371779 TNFi-treated, replicate 2, snRNA-seq
- GSM8371780 TNFi-treated, replicate 3, snRNA-seq
- GSM8371781 TNFi-treated, replicate 4, snRNA-seq
- GSM8371782 Negative CTL, replicate 1, snRNA-seq
- GSM8371783 Negative CTL, replicate 2, snRNA-seq
- GSM8371784 Negative CTL, replicate 3, snRNA-seq
- GSM8371785 Negative CTL, replicate 4, snRNA-seq
- GSE307773 Oncogenic MAPK signalling induces epithelial cell state change and therapeutic resistance in vivo [RNA-Seq] 175 samples shares therapeutic, epithelial
- GSE307774 Oncogenic MAPK signalling induces epithelial cell state change and therapeutic resistance in vivo [scRNA-Seq] 29 samples shares therapeutic, epithelial
- GSE223323 Enterocyte like differentiation defines metabolic gene signatures of CMS3 colorectal cancers and provides therapeutic vulnerability 148 samples shares therapeutic
- GSE234245 Multiomic Profile Integration Reveals Early Signatures of Amyotrophic Lateral Sclerosis and Suggests the MAPK Pathway as a Therapeutic Target [RNA-Seq] 79 samples shares therapeutic
- GSE280699 The mitochondrial-targeted peptide therapeutic elamipretide improves cardiac and skeletal muscle function during aging without detectable changes in tissue epigenetic or transcriptomic age [RNA-seq] 78 samples shares therapeutic
- GSE298799 Deconstructing the Intercellular Interactome in Vascular Dementia with Focal Ischemia for Therapeutic Applications 77 samples shares therapeutic
- GSE325852 Translatome profiling reveals opposing alterations in inhibitory and excitatory neurons of Fragile X mice and identifies EPAC2 as a therapeutic target 69 samples shares therapeutic
- GSE243008 Mitochondrial serine metabolism fuels epigenetic remodelling in osteoclast differentiation and is the main target of methotrexate 58 samples shares methotrexate
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.