Additional file 4 of Natural variation in the maternal and zygotic mRNA complements of the early embryo in Drosophila melanogaster

Additional file 4. Results showing differentially expressed genes within Zambia and Raleigh populations and between the two populations at both stage 2 and stage 5. Differential expression analysis was done using the DEseq2 (version 3.1) ⁠[49]⁠ package in R. Using DEseq2, we implemented the LRT (likelihood ratio test). For within- population analysis the replicates for each line were given the same label for the design matrix. For determining the differences between populations, we labeled lines as either Raleigh or Zambia in the design matrix and implemented the LRT test.