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P53 shapes genome-wide changes in small non-coding RNA expression during the human DNA damage response

ABSTRACT: Small RNA-seq on MCF10A, HCT116 and HCT116p53-/- cell lines after induction of DNA damage (5 Gy Irradiation).

ORGANISM(S): Homo sapiens

PROVIDER: GSE50064 | GEO | 2014/08/15

SECONDARY ACCESSION(S): PRJNA215929

REPOSITORIES: GEO

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p53 shapes genome-wide changes in small non-coding RNA expression during the human DNA damage response

Project description:Small RNA-seq on MCF10A, HCT116 and HCT116p53-/- cell lines after induction of DNA damage (5 Gy Irradiation). Small RNA-seq on MCF10A, HCT116 and HCT116p53-/- at 4 and 24 hours after induction of DNA damage (5 Gy Irradiation), done in duplicate with respective control (0 hour) using illumina Genome Analyzer IIx

2014-08-15 | E-GEOD-50064 | biostudies-arrayexpress

Gene Expression Profiling in Non-Human Primate Jejunum after Total-Body Irradiation

Project description:This is an experiment to study the effects of total body irradiation on intestinal gene expression. There are 24 male animals in the study; 4 controls, 10 animals received 6.7 Gy, 10 received 7.4 Gy. Animals were killed 4, 7 or 12 days after irradiation

2015-10-17 | GSE74107 | GEO

Gene Expression Profiling in Non-Human Primate Ileum after Total-Body Irradiation

2015-10-17 | GSE74109 | GEO

Gene Expression Profiling in Non-Human Primate Colon after Total-Body Irradiation

2015-10-17 | GSE74108 | GEO

Radiation Induced Pulmonary Fibrosis as a Model of Progressive Fibrosis: Contributions of DNA Damage, Inflammatory Response and Cellular Senescence Genes

Project description:Utilizing an established model of Radiation Induced Pulmonary Fibrosis, low input RNA sequencing was performed on whole lung cell suspensions obtained from 12.5 Gy thorax only radiation treated C57BL/6J mice and compareed to 0 Gy (Sham irradiation) age matched controls

2017-02-14 | GSE94852 | GEO

microRNA expression of K562, Me45 and HCT116, with or without p53 knock-out, treated with ionizing radiation.

Project description:MicroRNA expression was assessed in human cancer cells (K562, Me45, HCT116 wt and HCT116 p53-/-) treated with 4Gy of ionizing radiation. RNA was extracted from the cells 12 hours after irradiation and after 1h from non-treated controls.

2016-12-01 | E-MTAB-5197 | biostudies-arrayexpress

Ionizing radiation induced hair and skin damage

Project description:Skin samples from back region and footpads were analyzed in 8-10 week old mice. For back skin, the hair was plucked in order to induce active growing phase(anagen). After 9 days, the mice were irradiated for 5Gy IR. Krt17 knock out, p53 knock out, and wild type mice were compared. Samples were taken at time 0 (control), 6h, and 24h post-irradiation. For footpad skin, the mice were irradiated for 40 Gy IR. Krt17 knock out and wild type mice were compared. Samples were taken at time 0 (control), 3 d, 6 d, 9 d post-irradiation.

2020-12-22 | GSE163653 | GEO

transcriptomic assay on embryos after barley seeds gamma_irradiation-Molecular mechanisms of growth stimulation after low-dose irradiation of barley seeds

Project description:4plex_barley_2017_01 - transcriptomic assay on embryos after barley seeds gamma_irradiation - Why radiation exposure on seeds at low doses causes stimulation of plant growth after germination? - Barley dry seeds of variety “Nur” were irradiated by gamma-rays (Co-60) at doses 20 Gy (stimulatory) and 100 Gy (inhibitory). Immediately after irradiation we put seeds for germination to Petri dishes containing water filter paper; embryos were taken 2h after irradiation, embryos with embrionic roots were taken 24 and 48h after irradiation. The following comparisons have been made: non-irradiated (0 Gy), 2h vs. 20 Gy, 2h; 0 Gy, 24h vs. 20 Gy, 24h; 0 Gy, 48h vs. 20 Gy, 48h; 0 Gy, 24h vs. 100 Gy, 24h. Three independent biological replicates were used.

2019-12-01 | GSE117356 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of 0 and 5 Gy HuR binding RNAs

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

Transcription profiling of human cell lines K562, Me45 and HCT116 with or without p53 knock-out to study the effect of ionizing radiation

Project description:The objective of the experiment was to compare changes in the transcriptome induced by direct X-irradiation of cells, using the human K562 erythroleukemic, Me45 melanoma and HCT116 colon cancer cell lines. The transcript levels of K542 and Me45 RNA samples were measured using Affymetrix HG-U133A microarrays and for HCT116 with HGU 133A 2.0 in time points 1, 12, 24 h after irradiation and compared to the levels of RNA from control cells. Experiments were repeated twice for Me45 and K562 cells.

2010-09-28 | E-MEXP-2623 | biostudies-arrayexpress

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