Plants exhibit a robust transcriptional response to gamma radiation which includes the induction of transcripts required for homologous recombination and the suppression of transcripts that promote cell cycle progression. Various DNA damaging agents induce different spectra of DNA damage as well as collateral damage to other cellular components and therefore are not expected to provoke identical responses by the cell. Here we study the effects of two different types of ionizing radiation (IR) treatment HZE (1 GeV Fe26+ high mass high charge and high energy relativistic particles) and gamma photons on the transcriptome of Arabidopsis thaliana seedlings. Both types of IR induce small clusters of radicals that can result in the formation of double strand breaks (DSBs) but HZE also produces linear arrays of extremely clustered damage. We performed these experiments across a range of time points (1.5-24 h after irradiation) in both wild-type plants and in mutants defective in the DSB-sensing protein kinase ATM. The two types of IR exhibit a shared double strand break-repair-related damage response although they differ slightly in the timing degree and ATM-dependence of the response. The ATM-dependent DNA metabolism-related transcripts of the DSB response were also induced by other DNA damaging agents but were not induced by conventional stresses. Both Gamma and HZE irradiation induced at 24 h post-irradiation ATM-dependent transcripts associated with a variety of conventional stresses; these were overrepresented for pathogen response rather than DNA metabolism. In contrast only HZE-irradiated plants at 1.5 h after irradiation exhibited an additional and very extensive transcriptional response shared with plants experiencing extended night. This response was not apparent in gamma-irradiated plants. We treated 5-day-old WT and atm-1 seedlings of Arabidopsis thaliana with 100 Gy of Gamma radiation (over a span of 15 minutes) or 30 Gy of HZE (over a span of approximately 12 minutes). Gamma irradiations were completed at 8:40 am while HZE irradiations were conducted in two runs (due to space limitations) which were completed at 1:09 and 1:28pm respectively. Gamma treated seedlings were sampled at 10:10 am 11:40 am 2:55 pm 8:40 pm and 8:40 am. HZE treated seedlings were sampled at 2:39 pm 4:09 pm 7:24 pm 1:09 am and 1:09 pm. Un-irradiated WT and atm-1 control seedlings were sampled at 10:45 am on Day #1 and 9:15 am on Day #2. There are a total of 22 experimental or control conditions with two replicates per condition yielding 44 samples overall.