Coupling of MAPK output and lineage identity defines archetypal modes of TKI resistance in EGFR-mutant lung adenocarcinoma
Rendered analysis notebooks for:
Zatzman, M., Quintanal-Villalonga, A. et al, Coupling of MAPK output and lineage identity defines archetypal modes of TKI resistance in EGFR-mutant lung adenocarcinoma.
Overview
One notebook per main figure, each carrying the supplementary figures its legend points to, executed end to end against the deposited data. Code is folded by default — open any block to see what produced the panel above it.
Source, setup instructions, and the processing notebooks that document how the deposited objects were built are in the code repository: https://github.com/shahcompbio/egfr_nucseq.
Figure notebooks
In paper order:
| figure | notebook |
|---|---|
| Fig 1 — cohort and timeline | 01_cohort_metadata |
| Fig S2 — MSK-IMPACT panel sequencing | 31_impact_analysis |
| Fig 2, S3–S5 — phenotypic shifts | 90_figure2 |
| Fig 3, S6–S8 — LUAD deprogramming | 91_figure3 |
| Fig 4, S9 — MAPK coupling | 92_figure4 |
| Fig 4C–D, S7C, S9C — Lung Cancer Cell Atlas | 33_luca_analysis |
| Fig S9D, S9G — published transformation cohorts | 34_bulk_transformation |
| Fig 5, S10 — lineage plasticity | 93_figure5 |
| Fig 6, S11–S13 — Xenium spatial cohort | xenium/99_xenium_plots |
Data
| deposit | holds |
|---|---|
| GEO GSE292469 — single-nucleus RNA-seq | FASTQs and raw per-library count matrices for all 74 sequencing libraries, plus Series-level GSE292469_counts.h5 and GSE292469_cell_metadata.tsv.gz |
| GEO GSE342824 — Xenium in situ | per-section XeniumRanger output for all ten sections — counts, cell and nucleus boundaries, decoded transcripts, morphology images — plus xenium_cell_metadata.tsv.gz and the 389-target gene_panel.json |
| Zenodo — DOI at publication | the figure-reproduction bundle these notebooks run off: the three single-nucleus Seurat objects, the Xenium spatial object, and the derived result tables the notebooks read |
| CELLxGENE — link at publication | the cohort, epithelial and tumor histotime objects, for interactive browsing and download |
Every notebook here reads only from the Zenodo bundle.