scholarly journals Transcriptome and microRNAs Profiling Analysis of Huh7.5.1 Cells in Response to Hepatitis C Virus Infection

2021 ◽  
Vol 21 (8) ◽  
Author(s):  
Jinling Dong ◽  
Tiantian Wu ◽  
Ying Zhang ◽  
Zhihong Xie ◽  
Jie He
Keyword(s):  
Gene Expression ◽  
Next Generation Sequencing ◽  
Signaling Pathways ◽  
Cell Model ◽  
Regulation Of Gene Expression ◽  
Hcv Infection ◽  
Infection Model ◽  
Sequencing Analysis ◽  
Next Generation ◽  
Generation Sequencing

Background: There is a great need for further study on the mechanism of HCV infection or its pathopoiesis mechanism. Therefore, an HCV infection model was used to analyze the mechanisms of transcriptional and post-transcriptional regulation of gene expression. Methods: The detections of transcriptome and microRNAs expressions in Huh7.5.1 cells infected with JFH-1 were conducted with next-generation sequencing. Moreover, bioinformatics data were obtained. Results: There were 21,827,299, and 42,588,251 reads qualified Illumina read pairs obtained from JFH-1-infected (HCV) and non-infected (blank) Huh7.5.1 cells, respectively. Moreover, 678 and 1,041 mRNAs data with a length of 101 bp from HCV and blank Huh7.5.1 cells cDNA sequence were generated, respectively. The results of comparative transcriptome sequencing analysis declared 460 differentially expressed mRNAs in HCV-infected cells, including 152 upregulated mRNAs and 308 downregulated mRNAs (HCV vs. blank). Gene Ontology (GO) and KEGG pathway enrichment analyses indicated the involved pathways, such as MAPK, p53, and PI3K/Akt signaling pathways, as well as oocyte meiosis and pathways in cancer. Conclusions: Our work confirmed the transcriptome and microRNA data profiling from the cell model of HCV infection with JFH-1 using next-generation sequencing (NGS). Furthermore, the gene expression and regulation information or signaling pathways associated with the pathopoiesis mechanism of HCV infection were identified.

scholarly journals Dissection of gene regulatory networks in embryonic stem cells by means of high-throughput sequencing

2009 ◽  
Vol 390 (11) ◽  
Author(s):  
Christian Beisel ◽  
Renato Paro
Keyword(s):  
Gene Expression ◽  
Next Generation Sequencing ◽  
Molecular Mechanisms ◽  
Es Cells ◽  
Regulation Of Gene Expression ◽  
Embryonic Stem ◽  
Next Generation ◽  
Cell Fate Decisions ◽  
A Genome ◽  
Generation Sequencing

Abstract Transcription factor regulation of gene expression and chromatin-controlled epigenetic memory systems are closely cooperating in establishing the pluripotent state of embryonic stem (ES) cells and maintaining cell fate decisions throughout development of an organism. A thorough understanding of the regulatory transcriptional circuitry that rules the underlying plastic yet heritable gene expression programs in ES cells is of great importance. With the advent of next-generation sequencing technologies facilitating the quantitative assessment of functional genomics assays it is now feasible to interrogate transcription networks at a genome-wide scale. Here, we discuss the application of next-generation sequencing in elucidating the molecular mechanisms underlying ES cell function.

scholarly journals Differential Gene Expression in the Siphonophore Nanomia bijuga (Cnidaria) Assessed with Multiple Next-Generation Sequencing Workflows

PLoS ONE ◽  
2011 ◽  
Vol 6 (7) ◽  
pp. e22953 ◽  
Author(s):  
Stefan Siebert ◽  
Mark D. Robinson ◽  
Sophia C. Tintori ◽  
Freya Goetz ◽  
Rebecca R. Helm ◽  
...  
Keyword(s):  
Gene Expression ◽  
Next Generation Sequencing ◽  
Differential Gene Expression ◽  
Next Generation ◽  
Differential Gene ◽  
Generation Sequencing

Mutational profiling of acute myeloid leukemia with normal cytogenetics in Brazilian patients: the value of next-generation sequencing for genomic classification

2017 ◽  
Vol 65 (8) ◽  
pp. 1155-1158 ◽  
Author(s):  
Thiago Rodrigo de Noronha ◽  
Miguel Mitne-Neto ◽  
Maria de Lourdes Chauffaille
Keyword(s):  
Acute Myeloid Leukemia ◽  
Next Generation Sequencing ◽  
Myeloid Leukemia ◽  
Regulation Of Gene Expression ◽  
Uniparental Disomy ◽  
Driver Mutations ◽  
Next Generation ◽  
Normal Cytogenetics ◽  
Generation Sequencing ◽  
Acute Myeloid

Karyotype (KT) aberrations are important prognostic factors for acute myeloid leukemia (AML); however, around 50% of cases present normal results. Single nucleotide polymorphism array can detect chromosomal gains, losses or uniparental disomy that are invisible to KT, thus improving patients’ risk assessment. However, when both tests are normal, important driver mutations can be detected by the use of next-generation sequencing (NGS). Fourteen adult patients with AML with normal cytogenetics were investigated by NGS for 19 AML-related genes. Every patient presented at least one mutation:DNMT3Ain nine patients;IDH2in six;IDH1in three;NRASandNPM1in two; andTET2,ASXL1,PTPN11, andRUNX1in one patient. No mutations were found inFLT3,KIT,JAK2,CEBPA,GATA2,TP53,BRAF,CBL,KRAS,andWT1genes. Twelve patients (86%) had at least one mutation in genes related with DNA methylation (DNMT3A,IDH1,IDH2,andTET2), which is involved in regulation of gene expression and genomic stability. All patients could be reclassified based on genomic status and nine had their prognosis modified. In summary, NGS offers insights into the molecular pathogenesis and biology of cytogenetically normal AML in Brazilian patients, indicating that the prognosis could be further stratified by different mutation combinations. This study shows a different frequency of mutations in Brazilian population that should be confirmed.

scholarly journals DNA Methylation Landscape of 16 Canine Somatic Tissues by Methylation-Sensitive Restriction Enzyme-Based Next Generation Sequencing

2021 ◽  
Author(s):  
Jumpei Yamazaki ◽  
Yuki Matsumoto ◽  
Jaroslav Jelinek ◽  
Teita Ishizaki ◽  
Shingo Maeda ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Next Generation Sequencing ◽  
Restriction Enzyme ◽  
Companion Animals ◽  
Next Generation ◽  
Cpg Sites ◽  
Somatic Tissues ◽  
Methylation Sensitive Restriction Enzyme ◽  
Generation Sequencing

Abstract Background: DNA methylation plays important functions in gene expression regulation that is involved in individual development and various diseases. DNA methylation has been well studied in human and model organisms, but only limited data exist in companion animals like dog. Results: Using methylation-sensitive restriction enzyme-based next generation sequencing (Canine DREAM), we obtained canine DNA methylation maps from 16 somatic tissues. In total, we evaluated 130,861 CpG sites. The majority of CpG sites were either highly methylated (>70%, 52.5%-64.6% of all CpG sites analyzed) or unmethylated (<30%, 22.5%-28.0% of all CpG sites analyzed) which are methylation patterns similar to other species. The overall methylation status of CpG sites across the 32 methylomes were remarkably similar. However, the tissue types were clearly defined by principle component analysis and hierarchical clustering analysis with DNA methylome. We found 6416 CpG sites located closely at promoter region of genes and inverse correlation between DNA methylation and gene expression of these genes. Conclusions: Our study provides basic dataset for DNA methylation profiles in dogs.

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