IMC and scRNA-seq raw data of paired lung adenocarcinoma and healthy lung samples

Deposition of raw and processed data used in the publication:

The AICL-KLRF1 axis supports CD4-CD8 T cell communication and cytokine competence in pre-exhausted CD8+ T cells

Matthias; Barone1, Stefan; Peidli2,3, Anika; Neuschulz 1, Karla; Riesterer 1, Christina; Iwert1, Laia; Junquera1, Somesh; Sai4, Olufemi; Bolaji1, Diana; Bakoueva1, Christine; Appelt1, Benedikt; Obermayer5, Bertram; Klinger2,3, Alexandra; Trinks6, Anja; Sieber2, Nils; Blüthgen2,3, Birgit; Sawitzki#,1,7

# corresponding author: birgit.sawitzki@bih-charite.de

Affiliations:
1 Berlin Institute of Health (BIH) at Charité, Charité Universitätsmedizin Berlin, Berlin,
Germany
2 Institute of Pathology, Charité, Charité Universitätsmedizin Berlin, Berlin, Germany
3 Institute of Biology, Humbolt-Universität zu Berlin, Berlin, Germany
4 Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
5 Core Unit Bioinformatics (CUBI), Berlin Institute of Health (BIH) at Charité, Charité
Universitätsmedizin Berlin, Berlin, Germany
6 Bioportal Single Cells, Berlin Institute of Health at Charité-Universitätsmedizin Berlin,
Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117
Berlin, Germany
7 Der Simulierte Mensch, a science framework

DOI: 10.1038/s44319-026-00732-5

The deposition includes:

• IMC: raw TMA-wise .mcd and .txt output files from Hyperion, TMA zipped into "OT3 - Lung TMA block 1.zip"
• IMC: All masks generated via Ilastik - CellProfiler (Bodenmiller route with CellProfiler v3) zipped into "masks.zip"
• IMC: metadata file listing each ROI, TMA ("OT"), mouse_ID and condition as excel file "meta_IMlungpanel_CD3polygon.xlsx"
• IMC: processed raw data at single-cell resolution zipped into "IMC_cell.data.zip"
• scRNA-seq: processed anndata to create panels in Figure 6 and related Supplemental Figures zipped into "Fig6_processed_scRNAseq.zip"

IMC:

The data has been processed with a heavily adapted version of the Spectre code written in R language. Singe-cell data is both available here and in the Sawitzki github repo, where the code can be found. Here, "IMC_cell.data.zip" only contains the entire data set as .csv file "all.cells.csv". Be aware that this .csv file contains the positive controls of each TMA and is not gated for any immune cell types, nor does it include lymph node masks or spatial distances to tumor tissue.

scRNA-seq:

the data is originally published in Bischoff et al. but the samples were re-sequenced for 100 immune-targeted genes and re-analyzed. The code to reproduce the figure panels of the scRNA-seq data can be found on the Sawitzki github repo KLRF1-Tpex in "Figure Panels/Fig6"