GEO series

Regulatory Effects of Smoking Cessation on the Cellular Microenvironment and Differentially Expressed Genes in Precancerous Lesions of Pulmonary Nodules in Mice based on Single-Cell RNA-Sequencing and Immune Repertoire-Sequencing

GSE296378 Mus musculus (mouse) Single-cell RNA-seq 12 samples Submitted 2026/03/29 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 12 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: 12 samples: 12 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.

Summary (written by the submitters)

Smoking cessation is known to reduce lung cancer progression, but its impact on precancerous lesions remains largely unexplored. In this study, a smoking-induced mouse model of pulmonary precancerous lesions was established using 6-week benzo[a]pyrene (B[a]P) exposure. Lung nodules were identified through micro-MRI imaging and histopathological evaluation by H&E staining and fluorescence microscopy.

Read the full summary ↓

Smoking cessation interventions were applied for 4 and 8 weeks following lesion confirmation. Nodule size was quantified with Generic Medical Imaging software. Single-cell RNA sequencing (scRNA-seq) and immune repertoire sequencing (IR-seq) were performed to analyze immune cell composition, intercellular communication pathways, and receptor diversity. These approaches provide a comprehensive framework for investigating the cellular and molecular changes associated with smoking cessation in early lung lesion development.

This dataset

Open GSE296378 in finder → Find more mouse RNA-seq datasets →

Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE296378_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA1259022 and SRA study SRP583167. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

12 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 12 sample titles: 12 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.

Samples in this study

GSM8969402 BCR-seq of mouse lung tissue (Group A)
GSM8969403 BCR-seq of mouse lung tissue (Group B)
GSM8969404 BCR-seq of mouse lung tissue (Group C)
GSM8969405 Hashtag reads of mouse lung tissue (Group A)
GSM8969406 Hashtag reads of mouse lung tissue (Group B)
GSM8969407 Hashtag reads of mouse lung tissue (Group C)
GSM8969408 TCR-seq of mouse lung tissue (Group A)
GSM8969409 TCR-seq of mouse lung tissue (Group B)
GSM8969410 TCR-seq of mouse lung tissue (Group C)
GSM8969411 scRNA-seq of mouse lung tissue (Group A)
GSM8969412 scRNA-seq of mouse lung tissue (Group B)
GSM8969413 scRNA-seq of mouse lung tissue (Group C)

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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.