https://github.com/pwwang/immunopipe-liub-2022

Reanalysis of the scRNA-seq and scTCR-seq data from Liu, B., et al. 2022 using immunopipe.
https://github.com/pwwang/immunopipe-liub-2022

Last synced: 14 days ago
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Reanalysis of the scRNA-seq and scTCR-seq data from Liu, B., et al. 2022 using immunopipe.

• Host: GitHub
• URL: https://github.com/pwwang/immunopipe-liub-2022
• Owner: pwwang
• Created: 2023-12-30T06:28:01.000Z (about 1 year ago)
• Default Branch: master
• Last Pushed: 2024-07-28T01:02:23.000Z (5 months ago)
• Last Synced: 2024-12-10T04:27:03.402Z (24 days ago)
• Language: HTML
• Homepage:
• Size: 49.3 MB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# immunopipe-LiuB-2022

Reanalysis of the scRNA-seq and scTCR-seq data from [Liu, B., et al. 2022](https://www.nature.com/articles/s43018-021-00292-8) using [immunopipe](https://github.com/pwwang/immunopipe).

> [Liu, B., Hu, X., Feng, K., Gao, R., Xue, Z., Zhang, S., Zhang, Y., Corse, E., Hu, Y., Han, W., & Zhang, Z. (2022). Temporal single-cell tracing reveals clonal revival and expansion of precursor exhausted T cells during anti-PD-1 therapy in lung cancer. Nature Cancer, 3(1), 108-121.](https://www.nature.com/articles/s43018-021-00292-8)

## Data preparation

The data was downloaded from [GSE179994](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE179994), where 47 samples from 38 patients were sequenced with scRNA-seq and scTCR-seq.

See `prepare-data.sh` for details.

## Configuration

> [!NOTE]

> This is not a replication of the original paper, primarily due to the irreproducibility of the clustering results. This is a reanalysis of the data using [`immunopipe`](https://github.com/pwwang/immunopipe), showing the potential of the pipeline similar analyses listed in the paper.

>

The scRNA-seq data was prepared by following the instruction of the original paper. While selecting T cells, the TCR information was ignored (not mentioned in the paper). Instead, `CD3E`, `CD3D`, `CD3G` and `NKG7` were used to select T cells (and NK cells). The clusters were not annotated, so the clusters were named as `C1`, `C2`, etc. For further analysis, the clusters were selected by the expression of marker genes.

See details at `Immunopipe.config.toml`.

## Results/Reports

You can find the results in the `Immunopipe-output` directory.

The report can be found at [https://imp-liub-2022.pwwang.com/REPORTS](https://imp-liub-2022.pwwang.com/REPORTS).