Single-cell landscape of bronchoalveolar immune cells in patients with immune checkpoint inhibitor-related pneumonitis
Single-cell RNA-seq · human · 10 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
- 10 samples: 10 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
- Single-cell landscape of bronchoalveolar immune cells in patients with immune checkpoint inhibitor-related pneumonitisNPJ precision oncology · 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 GSE277136_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 PRJNA1160856 and SRA study SRP532544. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 10 sample titles: 10 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.
- GSM8514905 ICI-related pneumonitis patient 1, TCR-seq
- GSM8514906 ICI-related pneumonitis patient 1, scRNA-seq
- GSM8514907 ICI-related pneumonitis patient 2, TCR-seq
- GSM8514908 ICI-related pneumonitis patient 2, scRNA-seq
- GSM8514909 ICI-related pneumonitis patient 3, TCR-seq
- GSM8514910 ICI-related pneumonitis patient 3, scRNA-seq
- GSM8514911 ICI-related pneumonitis patient 4, TCR-seq
- GSM8514912 ICI-related pneumonitis patient 4, scRNA-seq
- GSM8514913 ICI-related pneumonitis patient 5, TCR-seq
- GSM8514914 ICI-related pneumonitis patient 5, scRNA-seq
- GSE243013 A single-cell atlas of immune heterogeneity in anti-PD1-treated non-small cell lung cancer 243 samples shares single-cell
- GSE334923 Single-cell RNA-seq atlas of peripheral blood and kidney graft immune cells in chronic antibody-mediated rejection 48 samples shares single-cell
- GSE269877 Single-cell RNA-sequencing of BCG naïve and recurrent non-muscle invasive bladder cancer reveals a CD6/ALCAM-mediated immune-suppressive pathway 38 samples shares single-cell
- GSE233844 Single-cell profiling reveals immune aberrations in progressive idiopathic pulmonary fibrosis 38 samples shares single-cell
- GSE328275 Single-cell RNA sequencing of CD45+ immune cells across primary tumor, sentinel tumor-draining lymph node, and axillary lymph node in treatment-naive triple-negative breast cancer 28 samples shares single-cell
- GSE277524 Single-cell dissection of multifocal bladder cancer reveals malignant and immune cells variation between primary and recurrence tumor lesions 10 samples shares single-cell
- GSE305971 Integrative single-cell analysis reveals malignant archetypes and proliferative hierarchies in multiple myeloma 2105 samples shares single-cell
- GSE227835 Single-cell RNA-seq data of human PBMC from Myasthenia Gravis patients 40 samples shares single-cell
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.