Efficient Identification of Multiple Pathways: RNA-Seq Analysis of Livers from 56Fe Ion Irradiated Mice
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA561415 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10011600_1.fastq.gz | Fastqsanger.gz | |||
| SRR10011600_2.fastq.gz | Fastqsanger.gz | |||
| SRR10011601_1.fastq.gz | Fastqsanger.gz | |||
| SRR10011601_2.fastq.gz | Fastqsanger.gz | |||
| SRR10011602_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 60 |
Similar Datasets
Project description:Background: mRNA interactions with each other and other signaling molecules define different biological pathways and functions. Researchers have been investigating various tools to analyze these types of interactions. In particular, gene co-expression network methods have proved useful in finding and analyzing these molecular interactions. Many different analytical pipelines to identify these interactions networks have been proposed with the aim of identifying an optimal partition of the network where the individual modules are neither too small to make any general inference or too large to be biologically interpretable. Results: In this study, we propose a new pipeline to perform gene co-expression network analysis. The proposed pipeline uses WGCNA, a widely used software to perform different aspects of gene co-expression network analysis and modularity maximization algorithm to analyze novel RNA-Seq data to understand the effects of low-dose 56Fe ion irradiation on the formation of hepatocellular carcinoma in mice. The network results along with experimental validation show that using WGCNA combined with Modularity provide a more biologically interpretable network in our dataset. Our pipeline showed better performance than the existing clustering algorithm in WGCNA in finding modules and identified a module with mitochondrial subunits that are supported by mitochondrial complex assay. Conclusions: We present a pipeline that can reduce the problem of parameter selection with the existing algorithm in WGCNA for comparable RNA-Seq datasets which may assist in future research to discover novel mRNA interactions and their downstream molecular effects.
2020-03-03 | GSE136165 | GEO
Project description:BACKGROUND:mRNA interaction with other mRNAs and other signaling molecules determine different biological pathways and functions. Gene co-expression network analysis methods have been widely used to identify correlation patterns between genes in various biological contexts (e.g., cancer, mouse genetics, yeast genetics). A challenge remains to identify an optimal partition of the networks where the individual modules (clusters) are neither too small to make any general inferences, nor too large to be biologically interpretable. Clustering thresholds for identification of modules are not systematically determined and depend on user-settable parameters requiring optimization. The absence of systematic threshold determination may result in suboptimal module identification and a large number of unassigned features. RESULTS:In this study, we propose a new pipeline to perform gene co-expression network analysis. The proposed pipeline employs WGCNA, a software widely used to perform different aspects of gene co-expression network analysis, and Modularity Maximization algorithm, to analyze novel RNA-Seq data to understand the effects of low-dose 56Fe ion irradiation on the formation of hepatocellular carcinoma in mice. The network results, along with experimental validation, show that using WGCNA combined with Modularity Maximization, provides a more biologically interpretable network in our dataset, than that obtainable using WGCNA alone. The proposed pipeline showed better performance than the existing clustering algorithm in WGCNA, and identified a module that was biologically validated by a mitochondrial complex I assay. CONCLUSIONS:We present a pipeline that can reduce the problem of parameter selection that occurs with the existing algorithm in WGCNA, for applicable RNA-Seq datasets. This may assist in the future discovery of novel mRNA interactions, and elucidation of their potential downstream molecular effects.
| S-EPMC7082965 | biostudies-literature
Project description:This study uses microarray analysis to examine the fate of multiple C-ion-irradiated tumors in vivo to gain a comprehensive overview of the changes in gene expression induced by C-ion irradiation. Four murine tumors were irradiated in vivo with C-ions at a single dose, and gamma-rays were used as a reference beam. Keywords: mouse squamous cell carcinoma and fibrosarcoma, carbon ion-irradiation, gamma-irradiation, resected sample, transplanted tissues
2008-06-09 | GSE11629 | GEO
Project description:In this study, carbon-ion beams generated via the heavy-ion medical accelerator in Chiba (HIMAC) were targeted to growing rice seedlings (7-days-old) to examine their effect on this genome model. Both physiological parameters, such as growth, and molecular events, specially the gene expression profiles were examined immediately after irradiation (at 270 Gy dose) by rice oligo (22K) DNA microarrays. Genome-wide transcriptional profiling of radiation-response genes in rice provides us with first report on how our radioactive environment affects a plant species. Keywords: Irradiation response
2008-03-29 | GSE9765 | GEO
Project description:In this study, carbon-ion beams generated via the heavy-ion medical accelerator in Chiba (HIMAC) were targeted to growing rice seedlings (7-days-old) to examine their effect on this genome model. Both physiological parameters, such as growth, and molecular events, specially the gene expression profiles were examined immediately after irradiation (at 270 Gy dose) by rice oligo (22K) DNA microarrays. Genome-wide transcriptional profiling of radiation-response genes in rice provides us with first report on how our radioactive environment affects a plant species. Experiment Overall Design: An in vivo 7-days-old rice seedling model system was used, where whole seedlings were used for exposure to the emitted radiation from HIMAC (carbon ion beams). Dye-swap or reverse labeling with Cy3 and Cy5 dyes procedure was applied followed by hybridization and wash processes, and the hybridized microarrays (G4138A) were scanned using a GenePix microarray scanner followed by the Gene Pix 4000 analysis application program for image analysis and data extraction processes. The GeneSpring Ver. 4 software was used for normalization.
2008-06-16 | E-GEOD-9765 | biostudies-arrayexpress
Project description:We have recently investigated the response of irradiated and bystander fibroblasts to heavy ions in confluent cultures exposed randomly to broadbeam and selectively to precision microbeam that target a predefined fraction of cells with counted number of particle(s), respectively, and found the difference in the time course of apoptosis induction and p53 phosphorylation between irradiated and bystander cells [Hamada MR2008]. In the present investigation, to further scrutinize the underpinnings of their temporally distinct responses, we set out to examine the gene expression changes in irradiated and bystander fibroblasts at a genome-wide level with the microarray analysis under the same experimental condition. We demonstrate that the gene expression profiles of bystander cells are substantially different from those of heavy ion-irradiated cells. Keywords: bystander effect, hour-time course cell number dependency, irradiation-dose response
2008-09-02 | GSE8993 | GEO
Project description:In the present study approximately 1 to 2 mm3 prostate tumor AT1 was inoculated subcutaneously in the right hind leg of adult male Copenhagen rats. When the tumor diameter exceeded 15 mm, tumors of 5 and 4 rats were irradiated with carbon ion radiation of 37 or 16Gy respectively. Tumors of 5 other rats were irradiated with photon radiation of 37Gy. One animal irradiated with 37 Gy carbon ion radiation and one animal irradiated with photon radiation was sacrificed 12h, 30h, 72h, 7d and 14d after irradiation respectively. One animal irradiated with 16 Gy photon radiation was sacrificed 12h, 60h, 7d and 14d after irradiation respectively. Non-irradiated animals were sacrificed at 60h time point. Tumors were dissected and frozen in liquid nitrogen immediately. Total RNA from tumor material was isolated using the NucleoSpin RNA L kit (#740962.20, Macherey-Nagel). Differential gene expression analysis was performed on the Agilent whole rat genome Oligo Microarray (44k) platform by comparative two dye hybridisation with dye-swaps.
2008-07-18 | E-TABM-481 | biostudies-arrayexpress
Project description:Linear energy transfer (LET) is an important factor affecting several aspects of the irradiation effect, e.g. cell survival and mutation frequency, making the heavy-ion beam an effective mutagen. To study the mechanisms behind LET-dependent effects, expression profiling was performed after heavy-ion beam irradiation of imbibed rice seeds. Array-based experiments at three time points (0.5, 1, 2 h after the irradiation) revealed that the number of up- or down-regulated genes was highest 2 h after irradiation. Array-based experiments with four different LETs at 2 h after irradiation identified LET-independent regulated genes that were up/down-regulated regardless of the value of LET; LET-dependently regulated genes, whose expression level increased with the rise of LET value, were also identified. Oryza sativa L. 'Nipponbare' seeds were imbibed for 3 days. The seeds were irradiated with 22.5 or 50 keV/μm C-ion or 63 or 80 keV/μm Ne-ion at a dose of 15 Gy. Gene expressions of irradiated and unirradiated embryos were measured at 2 hours after irradiation. Three independent experiments were performed at each time and LET.
2016-07-01 | E-GEOD-78994 | biostudies-arrayexpress
Project description:CEA_SGF:E00006# This set of experiments was performed in order to identify radiation responsive genes. For this, differentiated cultures derived from a single donor were irradiated at either 1 cGy, 2 Gy or sham-irradiated at T0 and total RNA extracts were prepared at 6 time points post-irradiation. Irradiated samples for each dose were hybridized seperately with sham-irradiated samples at the same time point. Each time point for each individual dose was assessed with two independent dye-swap hybridizations. Keywords: time-course
2004-11-01 | GSE1370 | GEO
Project description:Linear energy transfer (LET) is an important factor affecting several aspects of the irradiation effect, e.g. cell survival and mutation frequency, making the heavy-ion beam an effective mutagen. To study the mechanisms behind LET-dependent effects, expression profiling was performed after heavy-ion beam irradiation of imbibed rice seeds. Array-based experiments at three time points (0.5, 1, 2 h after the irradiation) revealed that the number of up- or down-regulated genes was highest 2 h after irradiation. Array-based experiments with four different LETs at 2 h after irradiation identified LET-independent regulated genes that were up/down-regulated regardless of the value of LET; LET-dependently regulated genes, whose expression level increased with the rise of LET value, were also identified. Oryza sativa L. 'Nipponbare' seeds were imbibed for 3 days. The seeds were irradiated with 22.5 or 50 keV/μm C-ion at a dose of 15 Gy. Gene expressions of irradiated and unirradiated embryos were measured at 0.5, 1, and 2 hours after irradiation. Three independent experiments were performed at each time and LET.
2016-07-01 | E-GEOD-78997 | biostudies-arrayexpress