310 High-throughput sequencing methods (RNA sequencing and Poly(A)-sequencing) to characterize full-length messenger RNA in transcriptionally silent bull sperm; Potential noninvasive measures of bull fertility

2017 ◽  
Vol 95 (suppl_2) ◽  
pp. 151-151
Author(s):  
B. L. Sartini
Keyword(s):  
Rna Sequencing ◽  
High Throughput ◽  
Messenger Rna ◽  
High Throughput Sequencing ◽  
Full Length ◽  
Bull Sperm

scholarly journals Single‐cell based high‐throughput sequencing of full‐length immunoglobulin heavy and light chain genes

2013 ◽  
Vol 44 (2) ◽  
pp. 597-603 ◽  
Author(s):  
Christian E. Busse ◽  
Irina Czogiel ◽  
Peter Braun ◽  
Peter F. Arndt ◽  
Hedda Wardemann
Keyword(s):  
Single Cell ◽  
High Throughput ◽  
Light Chain ◽  
High Throughput Sequencing ◽  
Full Length

scholarly journals Small RNA Expression Profiling by High-Throughput Sequencing: Implications of Enzymatic Manipulation

2012 ◽  
Vol 2012 ◽  
pp. 1-15 ◽  
Author(s):  
Fanglei Zhuang ◽  
Ryan T. Fuchs ◽  
G. Brett Robb
Keyword(s):  
High Throughput ◽  
Expression Profiling ◽  
Messenger Rna ◽  
High Throughput Sequencing ◽  
Biological Processes ◽  
Cellular Processes ◽  
Disease States ◽  
Powerful Approach ◽  
Sequencing Library ◽  
Rna Expression Profiling

Eukaryotic regulatory small RNAs (sRNAs) play significant roles in many fundamental cellular processes. As such, they have emerged as useful biomarkers for diseases and cell differentiation states. sRNA-based biomarkers outperform traditional messenger RNA-based biomarkers by testing fewer targets with greater accuracy and providing earlier detection for disease states. Therefore, expression profiling of sRNAs is fundamentally important to further advance the understanding of biological processes, as well as diagnosis and treatment of diseases. High-throughput sequencing (HTS) is a powerful approach for both sRNA discovery and expression profiling. Here, we discuss the general considerations for sRNA-based HTS profiling methods from RNA preparation to sequencing library construction, with a focus on the causes of systematic error. By examining the enzymatic manipulation steps of sRNA expression profiling, this paper aims to demystify current HTS-based sRNA profiling approaches and to aid researchers in the informed design and interpretation of profiling experiments.

Exosomal hsa-miR-129-2 and hsa-miR-889 from a 6-microRNA signature might be a potential biomarker for predicting prognosis of papillary thyroid carcinoma

2021 ◽  
Vol 24 ◽  
Author(s):  
Ying Xin ◽  
Kexin Meng ◽  
Haiwei Guo ◽  
Bin Chen ◽  
Chuanming Zheng ◽  
...  
Keyword(s):  
Papillary Thyroid Carcinoma ◽  
Thyroid Carcinoma ◽  
High Throughput ◽  
Messenger Rna ◽  
High Throughput Sequencing ◽  
The Cancer Genome Atlas ◽  
Papillary Thyroid ◽  
Control Groups ◽  
Potential Biomarker ◽  
And Control

Background: Papillary thyroid carcinoma (PTC) is a subtype of thyroid cancer with increasing incidence over time. Objective: This study aimed to build a risk score (RS) system for PTC patients. Methods: PTC microRNA (miRNA) and messenger RNA (mRNA) expression data were extracted from The Cancer Genome Atlas (TCGA) database. The 491 PTC samples were randomly divided into training and validation sets. Using the limma software package, differentially expressed mRNAs (DEGs) and miRNAs (DEMs) between the tumor and control groups were screened. In order to construct an RS system, a survival package was used to select independent miRNAs related to prognosis. Enrichment analysis was performed, and a miRNA-mRNA co-expression network was constructed. High-throughput sequencing was also used to verify the prognostic miRNAs in exosomes. Results: We found 1363 DEGs and 171 DEMs between the tumor and control groups. After identifying 26 DEMs that were significantly related to prognosis, 6 independent prognosis-associated miRNAs were selected to build an RS system. The areas under the curves of the overall survival rates of the training, validation, and entire sets were 0.847, 0.772, and 0.819, respectively. By conducting pathway analysis using the miRNA-mRNA co-expression network, one overlapping factor and five overlapping pathways were obtained. In addition, high-throughput sequencing revealed that the hsa-miR-129-2, hsa-miR-548j, hsa-miR-6734, and hsa-miR-889 expression levels in TCGA tumor tissues and exosomes were consistent, and those of hsa-miR-129-2 and hsa-miR-889 between patients and controls were significantly different in exosomes. Conclusion: The six-miRNA RS system in exosomes may comprise independent signatures for predicting PTC patient prognosis.

scholarly journals Nucleotide modifications in messenger RNA and their role in development and disease

2016 ◽  
Vol 44 (5) ◽  
pp. 1385-1393 ◽  
Author(s):  
Veronica Dezi ◽  
Chavdar Ivanov ◽  
Irmgard U. Haussmann ◽  
Matthias Soller
Keyword(s):  
High Throughput ◽  
Messenger Rna ◽  
Reverse Genetics ◽  
High Throughput Sequencing ◽  
Modified Nucleotides ◽  
Genes Encoding ◽  
Dynamic Landscape ◽  
Over 40 Years

Modified nucleotides in messenger RNA (mRNA) have been discovered over 40 years ago, but until recently little was known about which transcripts contain them and what their function is. High-throughput sequencing approaches revealed a dynamic landscape of the ‘Epitranscriptome’ for many mRNA modifications in various organisms from yeast to humans. Meanwhile, also many genes encoding mRNA-modifying enzymes and auxiliary proteins have been identified yielding functional insights by reverse genetics into their role in development and disease.

scholarly journals High-throughput and quantitative genome-wide messenger RNA sequencing for molecular phenotyping

BMC Genomics ◽  
2015 ◽  
Vol 16 (1) ◽  
Author(s):  
John E. Collins ◽  
Neha Wali ◽  
Ian M. Sealy ◽  
James A. Morris ◽  
Richard J. White ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
High Throughput ◽  
Messenger Rna ◽  
Genome Wide ◽  
Molecular Phenotyping

scholarly journals Unraveling the Heterogeneity and Ontogeny of Dendritic Cells Using Single-Cell RNA Sequencing

2021 ◽  
Vol 12 ◽  
Author(s):  
Binyao Chen ◽  
Lei Zhu ◽  
Shizhao Yang ◽  
Wenru Su
Keyword(s):  
Dendritic Cells ◽  
Single Cell ◽  
Rna Sequencing ◽  
Adaptive Immunity ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Future Trends ◽  
Innate And Adaptive Immunity ◽  
Sequencing Technologies ◽  
Single Cell Rna Sequencing

Dendritic cells (DCs) play essential roles in innate and adaptive immunity and show high heterogeneity and intricate ontogeny. Advances in high-throughput sequencing technologies, particularly single-cell RNA sequencing (scRNA-seq), have improved the understanding of DC subsets. In this review, we discuss in detail the remarkable perspectives in DC reclassification and ontogeny as revealed by scRNA-seq. Moreover, the heterogeneity and multifunction of DCs during diseases as determined by scRNA-seq are described. Finally, we provide insights into the challenges and future trends in scRNA-seq technologies and DC research.

scholarly journals Full-length immunoglobulin high-throughput sequencing reveals specific novel mutational patterns in POEMS syndrome

2019 ◽  
Author(s):  
Sébastien Bender ◽  
Vincent Javaugue ◽  
Alexis Saintamand ◽  
Maria Victoria Ayala ◽  
Mehdi Alizadeh ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Plasma Cell ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Clinical Manifestations ◽  
Diagnostic Value ◽  
Poems Syndrome ◽  
Full Length ◽  
Plasma Cell Dyscrasia ◽  
Multisystem Disease

AbstractPOEMS syndrome is a rare multisystem disease due to an underlying plasma cell (PC) dyscrasia. The pathophysiology of the disease remains unclear but the role of the monoclonal immunoglobulin (Ig) light chain (LC) is strongly suspected, due to the highly restrictive usage of two λ variable (V) domains (IGLV1-40 and IGLV1-44) and the general improvement of clinical manifestations following PC clone-targeted treatment. However, the diagnostic value of Ig LC sequencing, especially in case of incomplete forms of the disease, remains to be determined. Using a sensitive high-throughput Ig repertoire sequencing on RNA (RACE-RepSeq), we detected a λ LC monoclonal expansion in the bone marrow (BM) of 85% of patients with POEMS syndrome, including some in whom bone marrow tests routinely performed to diagnose plasma cell dyscrasia failed to detect λ+ monoclonal PCs. Twenty-four of the 30 LC clonal sequences found (80%) were derived from the IGLV1-40 and IGLV1-44 germline genes, two from the closely related IGLV1-36 gene, and all were associated with an IGLJ3*02 junction (J) gene, confirming the high restriction of VJ region usage in POEMS syndrome. RACE-RepSeq VJ full-length sequencing additionally revealed original mutational patterns, the strong specificity of which might crucially help establish or eliminate the diagnosis of POEMS syndrome in uncertain cases. Thus, RACE-RepSeq appears as a sensitive, rapid and specific tool to detect low-abundance PC clones in BM, and assign them to POEMS syndrome, with all the consequences for therapeutic options hereby.

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