Response of human lymphoblastoid cells to HZE (iron ions) or gamma-rays
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE16518 | GEO | 2011/04/01
SECONDARY ACCESSION(S): PRJNA122915
REPOSITORIES: GEO
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Project description:Transcriptional profiling of human lymphoblastoid TK6 cells comparing mock irradiated cells with cells exposed 24 hours previously to 1.67 Gy HZE (1 GeV/amu iron ions accelerated at the NASA Space Research Laboratory (NSRL) of Brookhaven National Laboratory) or 2.5 Gy 137Cs gamma rays. TK6 cells were mock irradiated or exposed to HZE or gamma-rays, and RNA was harvested 24 hours later. 3 biological replicates were independently grown and harvested during three different runs at the NSRL. One replicate per array.
2011-04-01 | E-GEOD-16518 | biostudies-arrayexpress
Project description:Transcriptional profiling of human lymphoblastoid TK6 cells comparing mock irradiaed cells resuspended in fresh untreated RPMI 1640 medium with cells resuspended in medium activated by exposure to 2.5 Gy HZE (1 GeV/amu iron ions accelerated at the NASA Space Research Laboratory (NSRL) of Brookhaven National Laboratory).
2011-04-01 | GSE16519 | GEO
Project description:Transcriptional profiling of human lymphoblastoid TK6 cells comparing mock irradiaed cells resuspended in fresh untreated RPMI 1640 medium with cells resuspended in medium activated by exposure to 2.5 Gy HZE (1 GeV/amu iron ions accelerated at the NASA Space Research Laboratory (NSRL) of Brookhaven National Laboratory). Two-condition experiment, mock irradiated vs. cells exposed to activated medium. 3 biological replicates were independently grown and harvested during three different runs at the NSRL. One replicate per array.
2011-04-01 | E-GEOD-16519 | biostudies-arrayexpress
Project description: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 M-bM-^@M-^\collateralM-bM-^@M-^] 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 M-bM-^@M-^\DSB responseM-bM-^@M-^] 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 M-bM-^@M-^\extended night.M-bM-^@M-^] 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.
2014-09-18 | E-GEOD-61484 | biostudies-arrayexpress
Project description:Transcriptional profiling of mammary tissue irradiated at 10 weeks of age with either 100 cGy sparsely ionizing gamma-rays, or 10 cGy or 30 cGy densely ionizing radiation (350 MeV/amu Si). Mammary tissue was collected 1 weeks, 4 weeks, and 12 weeks post-irradiation.
2013-11-30 | GSE48392 | GEO
Project description: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.
2014-09-18 | GSE61484 | GEO
Project description:Transcriptional profiling of mammary tissue irradiated at 10 weeks of age with either 100 cGy sparsely ionizing gamma-rays, or 10 cGy or 30 cGy densely ionizing radiation (350 MeV/amu Si). Mammary tissue was collected 1 weeks, 4 weeks, and 12 weeks post-irradiation. Four radiation treatment groups: sham, 100 cGy sparsely ionizing gamma-rays, 10 cGy or 30 cGy densely ionizing radiation (350 MeV/amu Si). Three time points post-irradiation (1, 4, and 12 weeks). Three or four replicates per time point.
2013-11-30 | E-GEOD-48392 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE16518: Response of human lymphoblastoid cells to HZE (iron ions) or gamma-rays GSE16519: Response of human lymphoblastoid cells to activated medium Refer to individual Series
2011-04-01 | E-GEOD-16525 | biostudies-arrayexpress
Project description:One of the health risks posed to astronauts during deep space flights is exposure to high charge, high-energy (HZE) ions (Z>13) which can lead to induction of hepatocellular carcinoma (HCC). We performed comparative RNA-Seq transcriptomic analysis to assess the carcinogenic effects of 600 MeV/n 56Fe (0.2 Gy), 1 GeV/n 16O (0.2 Gy), and 350 MeV/n 28Si (0.2 Gy) ions in a mouse model for radiation-induced hepatocellular carcinoma. C3H/HeNCrl mice were subjected to total body irradiation to simulate space HZE-irradiation environment and liver tissues were extracted at five different time points post-irradiation to investigate the time-dependent gradual carcinogenic response at the transcriptomic level. Our data demonstrated a clear difference in the effects of these HZE ions, particularly immunological, on the carcinogenic process of HCC, suggesting different molecular mechanisms of tumorigenesis. Also seen in this study was novel unmapped transcripts that were significantly affected by HZE. To investigate the biological functions of these transcripts, we used a machine learning technique known as self-organizing maps (SOMs) to characterize the transcriptome expression profiles of 60 samples (45 HZE-irradiated, 15 non-irradiated control) from liver tissues. A handful of localized modules in the maps emerged as groups of co-regulated and co-expressed transcripts. The functional context of these modules was discovered using overrepresentation analysis. We found that these spots typically contained enriched populations of transcripts related to specific immunological molecular processes. Taken together, these findings not only led to a better understanding of biological mechanisms underlying risks for HCC after HZE irradiation but also have important implications for discovery of potential countermeasures and identification of biomarkers of HZE-induced HCC.
2020-06-17 | GSE146254 | GEO
Project description:The purpose of the present work was to examine gene expression patterns in a rat keratinocyte line exposed to a 56Fe ion beam Experiment Overall Design: The cells were exposed to 1.01 geV/nucleon 56Fe ions generated by the NASA Space Radiation Laboratory facility. Data from Affymetrix rat microarrays (RAT 230_2) were processed by BRB ArrayTools 3.3.0 software, and the Gene Ontogeny (GO) database was utilized to categorize significantly responding genes.
2007-11-29 | E-GEOD-6299 | biostudies-arrayexpress