Experimental design for RNA extraction and RNA-Seq experiment in Conyza bonariensis glyphosate-resistant (GR) and -sensitive (GS) biotypes with (t1) and without (t0) glyphosate treatment. RNA samples 1–3: GR t0—untreated; RNA samples 4–6: GS t0—untreated; RNA samples 7–9: GS t1—RNA samples extracted at 24, 96, and 192 h after glyphosate treatment; RNA samples 10–12: GR t1—RNA extracted at 24, 96, 192, and 288 h after glyphosate treatment. RNA was extracted from a total of 27 plants and pooled according to each treatment. Three technical replicates were sequenced from each treatment (GR t0, GS t0, GS t1, and GR t1—a total of 12 libraries). Glyphosate rate of 1480 g ae ha−1.