Extended Data Fig. 9 |. Additional data for Atg12.

a, TEM photo showing increased number of autophagosomes (purple) and mitochondria (green) in Renca Atg12Δ cells compared to WT cells. Data represents a single experiment. b, Sectored scatter plots of gene-level quantile normalized NormZ scores (qNormZ) from WT and Atg12Δ cells propagated under CTL selection pressure. Significant negative and positive GIs (FDR < 5%) are coloured blue and yellow, respectively. Dashed line reflects median NormZ of GIs. c, Western blot depicting levels of select autophagy, NF-κβ and Nrf2 pathway-associated proteins in isogenic Renca–HA WT, Atg12Δ or Atg7Δ cells, as well as intergenic or Atg12 gRNA-transduced polyclonal KO Renca cell populations. Data represent a single experiment reflective of 3 independent biological replicates. d, Differential gene expression between TNF-treated WT and Atg12Δ Renca cells highlighting downregulated (purple; n = 190) and upregulated (orange; n = 251) genes (FDR < 0.05). Representative genes for the Reactome NF-κβ pathway (R-HSA-975138.1) are labelled (n = 12). Side box plots display mean fold change (where fold change = log₂(KO or WT read counts ± cytokine) − log₂(WT read counts)) of ER stress pathway genes between Atg12Δ, TNF-treated or Atg12Δ + TNF treatment conditions relative to WT cells. Boxes show the interquartile range (IQR, 25th to 75th percentile), with the median indicated by a line. The whiskers extend to the quartile ± 1.5 × IQR. Data representative of 3 independent biological replicates, and statistical significance was determined by a two-sided Student’s t-test between each treatment condition group.