High throughput sequencing of human fibroblast WS1 cells after 5 Gy X-ray irradiation
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PROVIDER: PRJNA396826 | ENA |
REPOSITORIES: ENA
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Project description:Purpose: The goal of this study was to compare the lncRNA and mRNA expression profile of human fibroblast WS1 cells between 0 Gy and 5 Gy X-ray irradiation. Methods: lncRNA and mRNA-sequencing of WS1 cells were generated using Illuminal Hiseq4000, RNA-seq reads were mapped to human genome hg19 by hisat2 software. Cuffdiff software was used to analysis the differentially expressed levels of LncRNA and mRNA FPKM. Results: We identified different expressed levels of 88780 lnRNA and 20311 mRNA transcripts in WS1 cells between 0 Gy and 5 Gy X-ay irradiation. Conclusion: Our study first revealed the detail of lncRNA and mRNA expression profiles of WS1 cells after 5Gy of X-Ray irradiation
2018-07-20 | GSE102145 | GEO
Project description:We report the application of RIP-sequencing technology for high-throughput profiling of ELAVL1 protein on the effect of lncRNA an mRNA in WS1 cells after 5 Gy X-ray irradiation
2018-07-20 | GSE102146 | GEO
Project description:This study aims to compared mRNA expression between IFI6-overexpressed WS1 cells and NC by RNA-Seq. In this study, WS1 cells were divided into two groups and each group had four repeats, one group was infected by IFI6-overexpressed lentivirus and another was infected by NC lentivirus. The two groups of cells were then irradiated with a single 5 Gy dose of radiation at a fixed rate of 1.15 Gy/min using an X-ray linear accelerator (Rad Source Technologies Inc., Suwanee, GA, USA). 24 hours post irradiation, WS1 cells from IFI6-overexpression and NC were collected and subjected to mRNA expression analysis.
2020-09-09 | GSE146527 | GEO
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of RNA. The goals of this study are to compare HuR binding RNAs between 0 or 5 Gy irradiation, and analyze its effect on RNA expression. Methods: Human skin fibroblast cell line WS1 cells were treated with 0 or 5 Gy irradiation. After 24 h, RNA expression was measured using using Illumina HiSeq4000. Meanwhile, RIP was performed using HuR antibody. HuR bound mRNAs after 0 or 5 Gy irradiation was measured using using Illumina HiSeq4000. Results: RIP-sequencing reveals HuR binding RNAs between 0 or 5 Gy irradiation in WS1 cells. RNA sequencing reveals dyeregulated RNAs between 0 and 5 Gy irradiation. Conclusions: Our study represents the first detailed analysis of HuR binding RNAs between 0 and 5 Gy irradiation generated by RNA-seq technology. This study contributes to our understanding of the role of HuR inresponse to radiation.
2019-02-22 | GSE111823 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2018-07-20 | GSE102147 | GEO
Project description:Hela cells were used to evaluate the protoporphytin IX (PpIX) effects on X-ray irradiation. Treatment conditions were (1) control group (untreated cells); (2) cells treated with 1 μg /ml PpIX for 6 hours; (3) cells irradiated with 3Gy X-rays; (4) cells treated with 1 μg /ml PpIX for 6 hours prior to irradiation with 3Gy X-rays. Hela cells gene expressions in 4 groups were measured at 24 hours after exposure to 0 and 3 Gy X-rays plus treatment with PpIX prior to irradiation.
2015-01-21 | E-GEOD-61805 | biostudies-arrayexpress
Project description:Exposure to radiation provokes cellular responses controlled in part by gene expression networks. MicroRNAs (miRNAs) are small non-coding RNAs which mostly regulate gene expression by degrading the messages or inhibiting translation. Here, we investigated changes in miRNA expression patterns after low (0.1 Gy) and high (2.0 Gy) doses of X-ray in human fibroblasts. At early (0.5 h) and late (6 and 24 h) time points, irradiation caused qualitative and quantitative differences in the down-regulation of miRNA levels, including miR-92b, 137, 660, and 656. A transient up-regulation of miRNAs was observed after 2 h post-irradiation following high doses of radiation, including miR-558 and 662. MicroRNA levels were inversely correlated with targets from mRNA and proteomic profiling after 2.0 Gy of radiation. MicroRNAs miR-579, 608, 548-3p, and 585 are noted for targeting genes involved in radioresponsive mechanisms, such as cell cycle checkpoint and apoptosis. We suggest here a model in which miRNAs may act as "hub" regulators of specific cellular responses, immediately down-regulated so as to stimulate DNA repair mechanisms, followed by up-regulation involved in suppressing apoptosis for cell survival. Taken together, miRNAs may mediate signaling pathways in sequential fashion in response to radiation, and may serve as biodosimetric markers of radiation exposure. The gene expression patterns in human fibroblasts after 2.0 Gy of low-LET radiation was determined at 2 and 24 hrs post-irradiation time in technical triplicates. Control non-irradiated samples were also prepared in triplicates.
2010-06-20 | E-GEOD-12647 | biostudies-arrayexpress
Project description:Arabidopsis cmt3 mutant showed neither DNA hypomethylation nor transcriptional activation of silenced repeats by gamma rays, which was found in wild type (WT). We used microarrays to compare the global transcriptional changes between the WT and cmt3 after the irradiation of 200 Gy. Transcriptions of transposition-related genes seemed to be differently affected in the WT and cmt3 by gamma rays, depending on the epigenetic codes of the genome. However, genome-wide transcriptions of the WT and cmt3 couldn't be positively correlated with the different levels of DNA methylation after the irradiation of 200 Gy.
2013-06-01 | GSE43947 | GEO
Project description:Exposure to radiation provokes cellular responses controlled in part by gene expression networks. MicroRNAs (miRNAs) are small non-coding RNAs which mostly regulate gene expression by degrading the messages or inhibiting translation. Here, we investigated changes in miRNA expression patterns after low (0.1 Gy) and high (2.0 Gy) doses of X-ray in human fibroblasts. At early (0.5 h) and late (6 and 24 h) time points, irradiation caused qualitative and quantitative differences in the down-regulation of miRNA levels, including miR-92b, 137, 660, and 656. A transient up-regulation of miRNAs was observed after 2 h post-irradiation following high doses of radiation, including miR-558 and 662. MicroRNA levels were inversely correlated with targets from mRNA and proteomic profiling after 2.0 Gy of radiation. MicroRNAs miR-579, 608, 548-3p, and 585 are noted for targeting genes involved in radioresponsive mechanisms, such as cell cycle checkpoint and apoptosis. We suggest here a model in which miRNAs may act as "hub" regulators of specific cellular responses, immediately down-regulated so as to stimulate DNA repair mechanisms, followed by up-regulation involved in suppressing apoptosis for cell survival. Taken together, miRNAs may mediate signaling pathways in sequential fashion in response to radiation, and may serve as biodosimetric markers of radiation exposure.
2008-09-02 | GSE12647 | GEO
Project description:In the current study, we investigated the gene expression response of blood cells of non-human primates that were total body irradiated with a 4 Gy dose. We isolated total RNA from peripheral blood at 3 days before irradiation, and then from the same animals on days 3, 5 and 7 days after irradiation. Using Agilent Rhesus microarrays, we identified genes that were significantly differentially expressed across the 7-day time course of this study. We identified common biological functions affected that persisted across the 7-day study.
2023-03-29 | GSE113478 | GEO