To explore the mechanism of Agaricus blazei Murrill enrichment of the heavy metal cadmium,we employed Illumina high-throughput sequencing to analyze the transcriptomes of A.blazei mycelia treated with and without exog...To explore the mechanism of Agaricus blazei Murrill enrichment of the heavy metal cadmium,we employed Illumina high-throughput sequencing to analyze the transcriptomes of A.blazei mycelia treated with and without exogenous cadmium addition,and then the differentially expressed genes(DEGs)of the strains with high and low cadmium enrichment between the control and cadmium treatment were screened out.The results showed that the DEGs were mainly involved in steroid biosynthesis,antibiotic biosynthesis,protein processing in endoplasmic reticulum,glutathione metabolism and other pathways.Carbon metabolism and glutathione metabolism may play an important role in the response of A.blazei mycelium to cadmium stress.展开更多
研究从大规模单细胞转录组测序数据出发,获得结直肠癌(colorectal cancer, CRC)中肠道内分泌细胞(enteroendocrine cell, EEC)的单细胞转录组图谱;对此转录组测序数据作差异表达、功能以及拟时序分析,结果提示肿瘤微环境中EEC发育与激...研究从大规模单细胞转录组测序数据出发,获得结直肠癌(colorectal cancer, CRC)中肠道内分泌细胞(enteroendocrine cell, EEC)的单细胞转录组图谱;对此转录组测序数据作差异表达、功能以及拟时序分析,结果提示肿瘤微环境中EEC发育与激素合成/分泌相关功能不全有关;结合肿瘤基因组图谱(The Cancer Genome Atlas, TCGA)和肿瘤药敏多组学数据库(Genomics of Drug Sensitivity in Cancer, GDSC)中CRC的bulk转录组测序数据、随访信息和药物测试数据,筛选出对CRC患者生存具有积极影响的生物学标志物——胰高血糖素(glucagon,GCG)基因;利用肿瘤细胞系药物测试数据探究了GCG基因在CRC治疗中的潜在应用价值。该研究为CRC的治疗提供了新的思路。展开更多
Bioinformatics methods for various RNA-seq data analyses are in fast evolution with the improvement of sequencing technologies. However, many challenges still exist in how to efficiently process the RNA-seq data to ob...Bioinformatics methods for various RNA-seq data analyses are in fast evolution with the improvement of sequencing technologies. However, many challenges still exist in how to efficiently process the RNA-seq data to obtain accurate and comprehensive results. Here we reviewed the strategies for improving diverse transcriptomic studies and the annotation of genetic variants based on RNA-seq data. Mapping RNA-seq reads to the genome and transcriptome represent two distinct methods for quantifying the expression of genes/transcripts. Besides the known genes annotated in current databases, many novel genes/transcripts(especially those long noncoding RNAs) still can be identified on the reference genome using RNA-seq. Moreover, owing to the incompleteness of current reference genomes, some novel genes are missing from them. Genome-guided and de novo transcriptome reconstruction are two effective and complementary strategies for identifying those novel genes/transcripts on or beyond the reference genome. In addition, integrating the genes of distinct databases to conduct transcriptomics and genetics studies can improve the results of corresponding analyses.展开更多
文摘To explore the mechanism of Agaricus blazei Murrill enrichment of the heavy metal cadmium,we employed Illumina high-throughput sequencing to analyze the transcriptomes of A.blazei mycelia treated with and without exogenous cadmium addition,and then the differentially expressed genes(DEGs)of the strains with high and low cadmium enrichment between the control and cadmium treatment were screened out.The results showed that the DEGs were mainly involved in steroid biosynthesis,antibiotic biosynthesis,protein processing in endoplasmic reticulum,glutathione metabolism and other pathways.Carbon metabolism and glutathione metabolism may play an important role in the response of A.blazei mycelium to cadmium stress.
文摘研究从大规模单细胞转录组测序数据出发,获得结直肠癌(colorectal cancer, CRC)中肠道内分泌细胞(enteroendocrine cell, EEC)的单细胞转录组图谱;对此转录组测序数据作差异表达、功能以及拟时序分析,结果提示肿瘤微环境中EEC发育与激素合成/分泌相关功能不全有关;结合肿瘤基因组图谱(The Cancer Genome Atlas, TCGA)和肿瘤药敏多组学数据库(Genomics of Drug Sensitivity in Cancer, GDSC)中CRC的bulk转录组测序数据、随访信息和药物测试数据,筛选出对CRC患者生存具有积极影响的生物学标志物——胰高血糖素(glucagon,GCG)基因;利用肿瘤细胞系药物测试数据探究了GCG基因在CRC治疗中的潜在应用价值。该研究为CRC的治疗提供了新的思路。
基金supported by the National High Technology Research and Development Program of China(2015AA020104)the China Human Proteome Project(2014DFB30010)+1 种基金the National Science Foundation of China(31471239,to Leming Shi)the 111 Project(B13016)
文摘Bioinformatics methods for various RNA-seq data analyses are in fast evolution with the improvement of sequencing technologies. However, many challenges still exist in how to efficiently process the RNA-seq data to obtain accurate and comprehensive results. Here we reviewed the strategies for improving diverse transcriptomic studies and the annotation of genetic variants based on RNA-seq data. Mapping RNA-seq reads to the genome and transcriptome represent two distinct methods for quantifying the expression of genes/transcripts. Besides the known genes annotated in current databases, many novel genes/transcripts(especially those long noncoding RNAs) still can be identified on the reference genome using RNA-seq. Moreover, owing to the incompleteness of current reference genomes, some novel genes are missing from them. Genome-guided and de novo transcriptome reconstruction are two effective and complementary strategies for identifying those novel genes/transcripts on or beyond the reference genome. In addition, integrating the genes of distinct databases to conduct transcriptomics and genetics studies can improve the results of corresponding analyses.
