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Illumina NGS RNA-seq and RRBS Sequencing on Spaceflight Mouse Retina

ABSTRACT: We reported the retinal transcriptome and methylome profiles of spaceflight and habitat control mice. The retinal transcrtiome was generated including 764 million paired-end 75x2 bp RNA-seq data. The methylome was generated including 788 million 75-bp RRBS DNA methylation data. We identified 177 differentially expressed genes (DEGs) induced by spaceflight based on the RNA-seq dataset, and 643 differentially methylated genes (DMGs) based on RRBS dataset. Functional enrichement analysis based on DEGs and DMGs revealed that spaceflight altered extracellular matrix component (EMC), cell to cell junction, inflammation pathway, wound-healing process, etc. Integration analysis based on transcriptome and methylome suggested that modifications on DNA methylation were correlated with transcriptome changes for several significant biological processes and/or pathways.

ORGANISM(S): Mus musculus

PROVIDER: GSE159771 | GEO | 2021/06/30

REPOSITORIES: GEO

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Illumina NGS RNA-seq and RRBS Sequencing on Rat Kidney

Project description:We reported the kidney transcriptome and methylome profiles of rat Brown Norway (BN) and Sprague Dawley (CD) strains at late pregnancy (day 18/21) compared to non-pregnancy. The renal transcriptome was characterized from 326 million single-end 100bp RNA-seq data. The methylome dataset included 234 million 75-bp RRBS DNA methylation reads. We identified 297 differentially expressed genes (DEGs) induced by pregnancy in CD rats and 174 DEGs induced in BN rats, based on the RNA-seq dataset. 237 of the 297 DEGs in CD pregnant rats and 114 of the 174 DEGs in BN pregnant rats are strain specific, indicating differential adaptation to pregnancy. Methylome data reveals that strain differences is the major factor in determining methylation differences. We also found that pregant BN showed higher methylation than non-pregnant BN at transcription starter site (TSS) and promoter regions. Functional analysis based on DEGs and DMGs revealed that pregnant BN rats showed renal transcriptomic changes that induce vitamin D deficiency and renal pro-inflammatory gene expression that can partly explain pregnancy-specific proteinuria. Integrated analysis based on transcriptome and methylome suggested that modifications on DNA methylation were correlated with transcriptome changes for several significant biological processes and/or pathways.

2022-06-22 | GSE173380 | GEO

Genome-wide profiling of DNA methylation at single-base resolution based on MeDIP-bisulfite high-throughput sequencing and ridge regression (MB)

Project description:Unraveling complexity of DNA methylome is essential to decipher DNA methylation mechanism in life. However, this has been subjected to technological constraints to balance between cost and accurate measurement of the DNA methylation level. In this study, by innovatively introducing C-hydroxylmethylated adapters, we have developed MeDIP-Bisulfite sequencing (MB-seq), which could obtain DNA methylome of repertoire CpGs at single-base resolution. We found MB-seq only costs 10% of MethylC-seq, but covers 85% of total CpGs in human genome. Unlike absolute methylation levels determined by MethylC-seq and RRBS, MB-seq presented relative methylation levels that are linearly inflated. This has enlightened us to develop a MB-seq corresponding correction method for methylation level based on ridge regression, which integrates the data of MB-seq and RRBS to predict the methylation level of total 28.2 million CpGs on human genome with high accuracy (Pearson correlation coefficient, PCC=0.90). Moreover, by employing MB-seq, we generated the DNA methylome of an ovarian epithelial cell line (T29) and its oncogenic counterpart (T29H), respectively. After ridge regression, we identified 131,790 differential methylation regions (DMRs) with high accuracy between T29 and T29H, far more than 7,567 obtained from RRBS. Taken together, our result demonstrated that the MB-seq combined with ridge regression is a wide applicable approach for profiling of DNA methylome.

2015-10-01 | GSE62279 | GEO

Genome-wide profiling of DNA methylation at single-base resolution based on MeDIP-bisulfite high-throughput sequencing and ridge regression (MethyC + MeDIP)

2015-10-01 | GSE62277 | GEO

Genome-wide profiling of DNA methylation at single-base resolution based on MeDIP-bisulfite high-throughput sequencing and ridge regression (RNA)

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Spaceflight causes changes in gene expression, photoreceptor integrity, and oxidative stress-related damage in the murine retina

Project description:Purpose:The purpose of this study was to determine whether the spaceflight environment induces oxidative damage on ocular structure and how gene expression profiles change during spaceflight. Methods: RNA sequencing, immunofluorescence, and microCT assays were performed on two groups of mice to assess the effects of spaceflight on the mammalian retina. Ten week old adult C57BL/6 mice was flown aboard the ISS for 35 days and returned to Earth alive. Ground control mice were maintained on Earth in identical flight hardware. Within 38 (+/-4) hours of splashdown, mice were euthanized and ocular tissues were collected for analysis. Results:RNA sequencing detected 600 differentially expressed genes in spaceflight retina. This set of differentially expressed genes is enriched for genes related to visual perception, the phototransduction pathway, and numerous retina and photoreceptor phenotype categories. Eleven of the differentially expressed genes are associated with the disease retinitis pigmentosa, a retinal disease characterized by dystrophy of the rods and cones of the photoreceptor layer. Analysis of differentially expressed transcription factors indicate changes in chromatin structure, offering clues to the causes of the phenotypic changes observed. Additionally, immunofluorescence assays showed degradation of cone photoreceptors and increased oxidative stress in the retina. Retinal thickness, as well as thickness of the retinal pigment epithelium and choroid layers, were significantly reduced after spaceflight. Conclusions: These results indicate that retinal performance may decrease over extended periods of spaceflight and cause visual impairment.

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