scholarly journals Differentially expressed circRNA and functional pathways in the hippocampus of epileptic mice based on next‐generation sequencing

2021 ◽  
Author(s):  
Xian‐Qiu Liao ◽  
Hai‐Chun Yu ◽  
Li‐Mei Diao ◽  
Ling Lu ◽  
Huan Li ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Differentially Expressed ◽  
Next Generation ◽  
Functional Pathways ◽  
Generation Sequencing

scholarly journals Uncontrolled Diabetes Mellitus Has No Major Influence on the Platelet Transcriptome

2018 ◽  
Vol 2018 ◽  
pp. 1-9 ◽  
Author(s):  
Thomas G. Nührenberg ◽  
Marco Cederqvist ◽  
Federico Marini ◽  
Christian Stratz ◽  
Björn A. Grüning ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Next Generation Sequencing ◽  
Platelet Reactivity ◽  
Platelet Rich Plasma ◽  
Expression Profiles ◽  
Bioinformatic Analysis ◽  
Differentially Expressed ◽  
Major Influence ◽  
Next Generation ◽  
Generation Sequencing

Background. Diabetes mellitus (DM) has been associated with increased platelet reactivity as well as increased levels of platelet RNAs in plasma. Here, we sought to evaluate whether the platelet transcriptome is altered in the presence of uncontrolled DM. Methods. Next-generation sequencing (NGS) was performed on platelet RNA for 5 patients with uncontrolled DM (HbA1c 9.0%) and 5 control patients (HbA1c 5.5%) with otherwise similar clinical characteristics. RNA was isolated from leucocyte-depleted platelet-rich plasma. Libraries of platelet RNAs were created separately for long RNAs after ribosomal depletion and for small RNAs from total RNA, followed by next-generation sequencing. Results. Platelets in both groups demonstrated RNA expression profiles characterized by absence of leukocyte-specific transcripts, high expression of well-known platelet transcripts, and in total 6,343 consistently detectable transcripts. Extensive statistical bioinformatic analysis yielded 12 genes with consistently differential expression at a lenient FDR < 0.1, thereof 8 protein-coding genes and 2 genes with known expression in platelets (MACF1 and ITGB3BP). Three of the four differentially expressed noncoding genes were YRNAs (RNY1, RNY3, and RNY4) which were all downregulated in DM. 23 miRNAs were differentially expressed between the two groups. Of the 13 miRNAs with decreased expression in the diabetic group, 8 belonged to the DLK1–DIO3 gene region on chromosome 14q32.2. Conclusions. In this study, uncontrolled DM had a remote impact on different components of the platelet transcriptome. Increased expression of MACF1, together with supporting predicted mRNA-miRNA interactions as well as reduced expression of RNYs in platelets, may reflect subclinical platelet activation in uncontrolled DM.

Identification of differentially expressed microRNAs in the skin of experimentally sensitized naturally affected atopic beagles by next-generation sequencing

2020 ◽  
Vol 72 (4) ◽  
pp. 241-250
Author(s):  
Domenico Santoro ◽  
Antonio Di Loria ◽  
Teresa Mirante ◽  
Duarte Mendes Oliveira ◽  
Carmelo Laudanna ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Differentially Expressed ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals miRNAs differentially expressed by next-generation sequencing in cord blood buffy coat samples of boys and girls

Epigenomics ◽  
2016 ◽  
Vol 8 (12) ◽  
pp. 1619-1635 ◽  
Author(s):  
Daneida Lizarraga ◽  
Karen Huen ◽  
Mary Combs ◽  
Maria Escudero-Fung ◽  
Brenda Eskenazi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Cord Blood ◽  
Buffy Coat ◽  
Differentially Expressed ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Transcriptomic analysis highlights cochlear inflammation associated with age-related hearing loss in C57BL/6 mice using next generation sequencing

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9737
Author(s):  
Zhongwu Su ◽  
Hao Xiong ◽  
Yi Liu ◽  
Jiaqi Pang ◽  
Hanqing Lin ◽  
...  
Keyword(s):  
Hearing Loss ◽  
Next Generation Sequencing ◽  
Molecular Mechanisms ◽  
Transcriptomic Analysis ◽  
Differentially Expressed ◽  
Next Generation ◽  
Age Related ◽  
Cochlear Inflammation ◽  
Age Related Hearing Loss ◽  
Generation Sequencing

Background In our aging society, age-related hearing loss (AHL) is the most common sensory disorder in old people. Much progress has been made in understanding the pathological process of AHL over the past few decades. However, the mechanism of cochlear degeneration during aging is still not fully understood. Methods Next generation sequencing technique was used to sequence the whole transcriptome of the cochlea of C57BL/6 mice, a mouse model of AHL. Differentially expressed genes (DEGs) were identified using the Cuffdiff software. GO and KEGG pathway enrichment analyses of the DEGs were implemented by using the GOseq R package and KOBAS software, respectively. Results A total of 731 genes (379 up- and 352 down-regulated) were revealed to be differentially expressed in the cochlea of aged mice compared to the young. Many genes associated with aging, apoptosis, necroptosis and particularly, inflammation were identified as being significantly modulated in the aged cochlea. GO and KEGG analyses of the upregulated DEGs revealed that the most enriched terms were associated with immune responses and inflammatory pathways, whereas many of the downregulated genes are involved in ion channel function and neuronal signaling. Real-time qPCR showed that H2O2 treatment significantly induced the expression of multiple inflammation and necroptosis-related genes in HEI-OC1 cells. Conclusion Using next generation sequencing, our transcriptomic analysis revealed the differences of gene expression pattern with age in the cochlea of C57BL/6 mice. Our study also revealed multiple immune and inflammatory transcriptomic changes during cochlear aging and provides new insights into the molecular mechanisms underlying cochlear inflammation in AHL.

scholarly journals Transcriptome Profiles Using Next-Generation Sequencing Reveal Liver Changes in the Early Stage of Diabetes in Tree Shrew (Tupaia belangeri chinensis)

2016 ◽  
Vol 2016 ◽  
pp. 1-15 ◽  
Author(s):  
Xiaoyun Wu ◽  
Haibo Xu ◽  
Zhiguo Zhang ◽  
Qing Chang ◽  
Shasha Liao ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Next Generation Sequencing ◽  
Early Stage ◽  
Tree Shrew ◽  
Differentially Expressed ◽  
Next Generation ◽  
Healthy Tree ◽  
Novel Treatments ◽  
Liver Changes ◽  
Generation Sequencing

Determining the liver changes during the early stages of diabetes is critical to understand the nature of the disease and development of novel treatments for it. Advances in the use of animal models and next-generation sequencing technologies offer a powerful tool in connection between liver changes and the diabetes. Here, we created a tree shrew diabetes model akin to type 1 diabetes by using streptozotocin to induce hyperglycemia and hyperlipidemia. Using RNA-seq, we compiled liver transcriptome profiles to determine the differentially expressed genes and to explore the role of hyperglycemia in liver changes. Our results, respectively, identified 14,060 and 14,335 genes in healthy tree shrews and those with diabetes, with 70 genes differentially expressed between the two groups. Gene orthology and KEGG annotation revealed that several of the main biological processes of these genes were related to translational processes, steroid metabolic processes, oxidative stress, inflammation, and hypertension, all of which are highly associated with diabetes and its complications. These results collectively suggest that STZ induces hyperglycemia in tree shrew and that hyperglycemia induced oxidative stress led to high expression of aldose reductase, inflammation, and even cell death in liver tissues during the early stage of diabetes.

scholarly journals Deduction of Novel Genes Potentially Involved in Keratinocytes of Type 2 Diabetes Using Next-Generation Sequencing and Bioinformatics Approaches

2019 ◽  
Vol 8 (1) ◽  
pp. 73 ◽  
Author(s):  
En-Shyh Lin ◽  
Wei-An Chang ◽  
Yang-Yi Chen ◽  
Ling-Yu Wu ◽  
Yi-Jen Chen ◽  
...  
Keyword(s):  
Immune Response ◽  
Next Generation Sequencing ◽  
Differentially Expressed Genes ◽  
Defense Response ◽  
Wound Repair ◽  
Immune Defense ◽  
Differentially Expressed ◽  
Diabetic Patients ◽  
Next Generation ◽  
Generation Sequencing

Keratinocytes constitute the major cell type of epidermis, which participates in re-epithelialization during wound repair and the immune defense response to pathogens. The aim of the current study was to explore the differentially expressed genes and novel microRNA (miRNA) regulations that are potentially involved in diabetic keratinocytes through next-generation sequencing (NGS) and bioinformatics approaches. A total of 420 differentially expressed genes between normal and diabetic keratinocytes were identified, and systematic bioinformatics analyses indicated that these differentially expressed genes were functionally enriched in interferon-alpha signaling, viral defense response, and immune response. Additionally, the potential miR-340-3p-DTX3L interaction that has been systematically validated in miRNA prediction databases was proposed to participate in the disrupted skin homeostasis, altering the defense and immune response of diabetic skin. The findings may provide new insights into understanding the pathogenesis of epidermal pathologies in diabetic patients and targeting novel molecules to advance diabetic skin care in clinical practice.

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