Transcriptomic Profiling and Pathway Analysis of Mesenchymal Stem Cells following Low Dose-Rate Radiation Exposure
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA922495 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23035173_1.fastq.gz | Fastqsanger.gz | |||
| SRR23035173_2.fastq.gz | Fastqsanger.gz | |||
| SRR23035174_1.fastq.gz | Fastqsanger.gz | |||
| SRR23035174_2.fastq.gz | Fastqsanger.gz | |||
| SRR23035175_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 48 |
Similar Datasets
Project description:Radiation biodosimetry can play a critical role in the response to a large-scale radiologic emergency, and gene expression profiles have shown promise for providing biodosimetric information. This study was designed to test if gene expression could be used to distinguish between doses received from acute exposures and more protracted exposures, such as those that would result from fallout. Mice were exposed to whole body X-rays at low dose rate (LDR, 3.09 mGy/min) for 6, 12, or 24 hours (1.1, 2.2, or 4.4 Gy), or to equivalent doses delivered at high dose rate (HDR, 1.03 Gy/min). Global gene expression was measured in their blood 24 h after the start of exposure, and genes with the potential to classify samples by radiation dose and dose rate were identified.
2015-05-14 | GSE62623 | GEO
Project description:Radiation biodosimetry can play a critical role in the response to a large-scale radiologic emergency, and gene expression profiles have shown promise for providing biodosimetric information. This study was designed to test if gene expression could be used to distinguish between doses received from acute exposures and more protracted exposures, such as those that would result from fallout. Mice were exposed to whole body X-rays at low dose rate (LDR, 3.09 mGy/min) for 6, 12, or 24 hours (1.1, 2.2, or 4.4 Gy), or to equivalent doses delivered at high dose rate (HDR, 1.03 Gy/min). Global gene expression was measured in their blood 24 h after the start of exposure, and genes with the potential to classify samples by radiation dose and dose rate were identified. Data consist of 48 samples, representing 6 independent samples each from 3 doses delivered as either acute or low dose rate x-rays, plus 12 controls representing both acute and low dose rate sham treatments.
2015-05-14 | E-GEOD-62623 | biostudies-arrayexpress
Project description:Low-dose radiation refers to exposure to ionizing radiation at levels that are generally considered safe and not expected to cause immediate health effects. However, the effects of low-dose radiation are still not fully understood and research in this area is ongoing. In this study, we investigated changes in gene expression in diabetic human aortic endothelial cells (T2D-HAECs) derived from type 2 diabetes patients. To this end, we used RNA-seq to profile the transcriptomes of cells exposed to varying doses of low-dose radiation (0.1Gy, 0.5Gy, and 2.0Gy) and compared them to a control group with no radiation exposure. Differentially expressed genes and enriched pathways were identified using the DESeq2 and gene set enrichment analysis (GSEA) methods, respectively. The data generated in this study are publicly available through the gene expression omnibus (GEO) database. This study provides a valuable resource for studying the effects of low-dose radiation on T2D-HAECs and can contribute to a better understanding of the potential human health risks associated with low-dose radiation exposure.
2023-04-07 | GSE228572 | GEO
Project description:Using total RNAseq, we examined gene expression differences in MSC exposed to 0.66 cGy/h for 1 and 2 weeks, for a total of 1 and 2 Gy radiation.
2023-06-01 | GSE222541 | GEO
Project description:Expression profiles in mouse liver exposed to long-term gamma-irradiation were examined to assess in vivo effects of low dose-rate radiation. Three groups of male C57BL/6J mice were exposed to whole body irradiation at dose-rates of 17-20 mGy/day, 0.86-1.0 mGy/day or 0.042-0.050 mGy/day for 401-485 days (cumulative doses were approximately 8 Gy, 0.4 Gy or 0.02 Gy, respectively). Expression profiles were produced for RNA isolated from irradiated individual animals and for pooled RNA from sham-irradiated 3 animals for control. The expression levels of 6 irradiated animals for each dose were compared individually with those of 2 pooled controls (3 irradiated samples to one pooled control in first and second experiments).
2011-01-01 | GSE20562 | GEO
Project description:Background: The effects of dose-rate and its implications on radiation biodosimetry methods are not well studied in the context of large-scale radiological scenarios. There are significant health risks to individuals exposed to an acute dose in such an event, but the most realistic scenario would be a combination of exposure to both high and low dose-rates, from both external and internal radioactivity. It is important therefore, to understand the biological response to prolonged exposure; and further, discover biomarkers that can be used to estimate the extent of damage from low-dose rate exposure and propose appropriate clinical treatment. Methods: We irradiated human whole blood ex vivo to three doses, 0.56 Gy, 2.25 Gy and 4.45 Gy, using two dose rates: 1.1Gy/min and 3.1mGy/min. After 24 hours, we isolated RNA from blood cells and hybridized these to Agilent Whole Human genome microarrays. We validated the microarray results using qRT-PCR. Results: Microarray results showed that there were 454 significantly differentially expressed genes after prolonged exposure to all doses. After acute exposure, 598 genes were differentially expressed to all doses combined. Gene ontology terms enriched in both sets of genes were related to immune processes and B cell mediated immunity. Genes responding to acute exposure was also enriched in functions related to natural killer cell activation and cell-to-cell signaling. As expected, p53 pathway was found to be significantly enriched at all doses and by both dose-rates of radiation. Prediction algorithms were able to distinguish between low dose-rate and acute exposures, on the basis of a group of genes. These maybe candidates for preliminary testing as markers for differences in gene expression based on dose-rate. Radiation induced gene expression was measured in ex vivo irradiated human blood, at the 24hr time point after irradiation. Doses (0.56 Gy, 2.2 Gy and 4.45 Gy) were delivered by two dose rates, acute dose rate of 1Gy/min and low dose rate of 3.1 mGy/min.
2015-04-28 | E-GEOD-65292 | biostudies-arrayexpress
Project description:Background: The effects of dose-rate and its implications on radiation biodosimetry methods are not well studied in the context of large-scale radiological scenarios. There are significant health risks to individuals exposed to an acute dose in such an event, but the most realistic scenario would be a combination of exposure to both high and low dose-rates, from both external and internal radioactivity. It is important therefore, to understand the biological response to prolonged exposure; and further, discover biomarkers that can be used to estimate the extent of damage from low-dose rate exposure and propose appropriate clinical treatment. Methods: We irradiated human whole blood ex vivo to three doses, 0.56 Gy, 2.25 Gy and 4.45 Gy, using two dose rates: 1.1Gy/min and 3.1mGy/min. After 24 hours, we isolated RNA from blood cells and hybridized these to Agilent Whole Human genome microarrays. We validated the microarray results using qRT-PCR. Results: Microarray results showed that there were 454 significantly differentially expressed genes after prolonged exposure to all doses. After acute exposure, 598 genes were differentially expressed to all doses combined. Gene ontology terms enriched in both sets of genes were related to immune processes and B cell mediated immunity. Genes responding to acute exposure was also enriched in functions related to natural killer cell activation and cell-to-cell signaling. As expected, p53 pathway was found to be significantly enriched at all doses and by both dose-rates of radiation. Prediction algorithms were able to distinguish between low dose-rate and acute exposures, on the basis of a group of genes. These maybe candidates for preliminary testing as markers for differences in gene expression based on dose-rate.
2015-04-28 | GSE65292 | GEO
Project description:Expression profiles in mouse liver exposed to long-term gamma-irradiation were examined to assess in vivo effects of low dose-rate radiation. Three groups of male C57BL/6J mice were exposed to whole body irradiation at dose-rates of 17-20 mGy/day, 0.86-1.0 mGy/day or 0.042-0.050 mGy/day for 401-485 days (cumulative doses were approximately 8 Gy, 0.4 Gy or 0.02 Gy, respectively). Expression profiles were produced for RNA isolated from irradiated individual animals and for pooled RNA from sham-irradiated 3 animals for control. The expression levels of 6 irradiated animals for each dose were compared individually with those of 2 pooled controls (3 irradiated samples to one pooled control in first and second experiments). The experiments were conducted twice at similar dose-rates. In the first experiment, three groups of 8 weeks old male C57BL/6J mice were exposed to whole body irradiation at dose-rates of either 16.6 mGy/day (H1), 0.858 mGy/day (M1) or 0.042 mGy/day (L1) for 485 days (cumulative doses were 8030 mGy, 416 mGy or 20.6 mGy, respectively). In the second experiment, the doe-rates were slightly elevated as 20.0 mGy/day (H2), 1.000 mGy/day (M2) or 0.050 mGy/day (L2) for 401 days (doses were 8015 mGy, 401 mGy or 20 mGy, respectively). A group of control unirradiated mice were set for each experiment (C1, C2).
2011-01-01 | E-GEOD-20562 | biostudies-arrayexpress
Project description:One of the most likely risks astronauts on long duration space missions face is exposure to ionizing radiation associated with highly energetic and charged heavy (HZE) particles. Since access to medical expertise on such a mission is limited at best, early diagnosis and mitigation of such exposure is critical. In order to accurately determine the time since exposure and dosage of exposure, dose- and time-dependent “biomarkers” are needed. Therefore, we performed a dose- and time-course transcriptional analysis for radiation exposure at 0, 0.15, 0.30, and 1.5 Gy with corresponding time points at 1 hour (hr) post-exposure as well as 2 hr and 6 hr using Affymetrix® Human PrimeArrayTM chips. The analysis of our data suggests a set of sensitive genetic biomarkers specific to each radiation level as well as generic radiation response biomarkers. Upregulated biomarkers can then be used within lab-on-a-chip (LOC) systems to detect exposure to ionizing radiation.
2017-12-01 | GSE63952 | GEO
Project description:Measuring global gene expression using cDNA or oligonucleotide microarrays is an effective approach to understanding the complex mechanisms of the effects of radiation. However, few studies have been carried out that investigate gene expression in vivo after prolonged exposure to low-dose-rate radiation. In this study, C57BL/6J mice were continuously irradiated with γ-rays for 485 days at dose-rates of 0.032 – 13 μGy/min. Gene expression profiles in the kidney and testis from irradiated and unirradiated mice were analyzed, and differentially expressed genes were identified. A combination of pathway analysis and hierarchical clustering of differentially expressed genes revealed that expression of genes involved in mitochondrial oxidative phosphorylation was elevated in the kidney after irradiation at the dose-rates of 0.65 μGy/min and 13 μGy/min. Expression of cell cycle-associated genes was not profoundly modulated in the kidney, in contrast to the response to acute irradiation, suggesting a threshold in the dose-rate for modulation of the expression of cell cycle-related genes in vivo following exposure to radiation. We demonstrated that changes to the gene expression profile in the testis were largely different from those in the kidney. The Gene Ontology categories “DNA metabolism”, “response to DNA damage” and “DNA replication” overlapped significantly with the clusters of genes whose expression decreased with an increase in the dose-rate to the testis. These observations provide a fundamental insight into the organ-specific responses to low-dose-rate radiation. Key Words: kidney, low-dose-rate, radiation, microarray, mitochondrial oxidative phosphorylation, testis
2009-05-27 | GSE14290 | GEO