KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Critical commercial assays
TruSeq Stranded mRNA Sample Prep Kit	Illumina	20020594
Bioanalyzer HS DNA	Agilent	5067–4626
Qubit RNA BR	ThermoFisher	Q32852
RNA ScreenTape	Agilent	5067–5576
Quick-RNA Miniprep	Zymogen	R1054
Direct-Zol RNA Miniprep	Zymogen	R2050
ATAC-seq Kit	Active Motif	53150
ExoRNeasy Serum/Plasma Maxi Kit	Qiagen	77064
Smart Seq HT mRNA Sample Prep Kit	Takara	634456
Deposited data
AALE RNA-seq and ATAC-seq raw data	This paper	GEO: GSE120566
HBEC RNA-seq raw data	This paper	GEO: GSE120566
A549 ZNF overexpression data	Ito et al. (2020)	GEO: GSE78099
GENCODE v35	Frankish et al. (2021)	https://www.gencodegenes.org/human/release_35.html
TCGA counts data	UCSC Xena Browser	https://xenabrowser.net/datapages/?cohort=TCGA%20TARGET%20GTEx&addHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443
ZNF target database & scores	Imbeault et al. (2017)	https://static-content.springer.com/esm/art%3A10.1038%2Fnature21683/MediaObjects/41586_2017_BFnature21683_MOESM107_ESM.xlsx
Transposable element reference	UCSC Genome Browser	https://genome.ucsc.edu/cgi-bin/hgTables
KZNF binding motifs	Barazandeh et al. (2018)	http://kznfmotifs.ccbr.utoronto.ca/index.html
Experimental models: Cell lines
Human lung airway epithelial cells (AALE)	Lundberg et al. (2002)	N/A
Human lung bronchial epithelial cells (HBEC3kt)	Harold Varmus lab	RRID:CVCL_X491
Recombinant DNA
pBABE-FLAG-KRAS(G12D) Zeo	Addgene	RRID:Addgene_58902
pBABE-mCherry Puro	Lu et al. (2017)	RRID:Addgene_25896
pLenti6/V5-GW/lacZ	John D. Minna lab, Vikis et al. (2007), ThermoFisher	V49610
pLenti-KRASV12	John D. Minna lab, Vikis et al. (2007), Sato et al. (2013)	Backbone: V49610; Sequence: RRID:Addgene_12544
Software and algorithms
FastQC (0.11.9)	https://www.bioinformatics.babraham.ac.uk/projects/fastqc/	https://github.com/s-andrews/FastQC/releases/tag/v0.11.9t
Original code	This paper	https://doi.org/10.5281/zenodo.6618294
Trimmomatic (0.39)	Bolger et al. (2014)	http://www.usadellab.org/cms/?page=trimmomatic
Salmon (1.3.0)	Patro et al. (2017)	https://salmon.readthedocs.io/en/latest/
nf-core/atacseq	https://github.com/nf-core/atacseq/tree/1.2.1	https://zenodo.org/record/3965985
R (4.1.1)	https://www.R-project.org/	R version 4.1.1 (2021–08-10) – ‘‘Kick Things’’
R – DESeq2	Love et al. (2014)	https://doi.org/10.18129/B9.bioc.DESeq2
R – apeglm	Zhu et al. (2019)	https://doi.org/10.18129/B9.bioc.apeglm
R – fgsea	Korotkevich et al. (2016)	https://doi.org/10.18129/B9.bioc.fgsea
R – tximeta	Love et al. (2020)	https://doi.org/10.18129/B9.bioc.tximeta
R – stats	R core team	https://www.R-project.org/
R – msigdbr	Dolgalev (2022)	https://cran.r-project.org/web/packages/msigdbr/index.html
R – GenomicRanges	Lawrence et al. (2013)	https://doi.org/10.18129/B9.bioc.GenomicRanges
R – BSgenome.Hsapiens.UCSC.hg38	Bioconductor	https://doi.org/10.18129/B9.bioc.BSgenome.Hsapiens.UCSC.hg38
R – survival	Therneau (2022)	https://cran.r-project.org/package=survival
R – rGREAT	Bioconductor	https://doi.org/10.18129/B9.bioc.rGREAT
R – MEMES	Nystrom and McKay, 2021	https://doi.org/10.18129/B9.bioc.memes
R – bamsignals	Bioconductor	https://doi.org/10.18129/B9.bioc.bamsignals
R – MotifDB	Bioconductor	https://doi.org/10.18129/B9.bioc.MotifDb
R – UniversalMotif	Bioconductor	https://doi.org/10.18129/B9.bioc.universalmotif
R – ComplexHeatmap	Gu et al. (2016)	https://doi.org/10.18129/B9.bioc.ComplexHeatmap
Other
HTML code notebook, repo	This paper	https://github.com/rreggiar/aale-KRAS-G12-transformation