scholarly journals QsRNA-seq: a method for high-throughput profiling and quantifying small RNAs

2018 ◽  
Author(s):  
Alla Fishman ◽  
Dean Light ◽  
Ayelet T. Lamm
Keyword(s):  
High Throughput ◽  
Small Rnas ◽  
High Throughput Sequencing ◽  
Developmental Stages ◽  
Biological Research ◽  
C Elegans ◽  
Cellular Processes ◽  
Repetitive Nature ◽  
Developmental Role ◽  
Non Coding Rnas

The finding that small non-coding RNAs (sRNAs) can affect cellular processes by regulating gene expression had a significant impact on biological research and clinical diagnosis. Yet, the ability to quantify and profile sRNAs, specifically miRNAs, using high-throughput sequencing is especially challenging because of their small size and repetitive nature. We developed QsRNA-seq, a method for preparation of sRNA libraries for high-throughput sequencing that overcomes this difficulty by enabling separation of fragments shorter than 100nt long that differ only by 20nt in length. The method supports using unique molecular identifiers for quantification. We show that QsRNA-seq gives very accurate, comprehensive and reproducible results. Using QsRNA-seq to study the miRNA repertoire in C. elegans embryo and L4 larval developmental stages, enabled extending the list of miRNAs that are expressed in a developmental-specific manner. Interestingly, we found that miRNAs 23nt long are predominantly expressed in developmental stage L4, suggesting a possible connection between the length of miRNA and its developmental role.

scholarly journals The high-throughput sequencing of small RNAs profiling in wide hybridisation and allopolyploidisation between Brassica rapa and Brassica nigra

Genomics Data ◽  
2015 ◽  
Vol 3 ◽  
pp. 1-3 ◽  
Author(s):  
Muhammad Awais Ghani ◽  
Junxing Li ◽  
Linli Rao ◽  
Muhammad Ammar Raza ◽  
Liwen Cao ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
High Throughput ◽  
Small Rnas ◽  
High Throughput Sequencing ◽  
Brassica Nigra ◽  
Wide Hybridisation

scholarly journals High-Throughput Sequencing is a Crucial Tool to Investigate the Contribution of Human Endogenous Retroviruses (HERVs) to Human Biology and Development

Viruses ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 633 ◽  
Author(s):  
Maria Paola Pisano ◽  
Nicole Grandi ◽  
Enzo Tramontano
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Developmental Stages ◽  
Large Fraction ◽  
Expression Patterns ◽  
Cell Types ◽  
Endogenous Retroviruses ◽  
Human Endogenous Retroviruses ◽  
Retroviral Infections ◽  
The Impact

Human Endogenous retroviruses (HERVs) are remnants of ancient retroviral infections that represent a large fraction of our genome. Their transcriptional activity is finely regulated in early developmental stages and their expression is modulated in different cell types and tissues. Such activity has an impact on human physiology and pathology that is only partially understood up to date. Novel high-throughput sequencing tools have recently allowed for a great advancement in elucidating the various HERV expression patterns in different tissues as well as the mechanisms controlling their transcription, and overall, have helped in gaining better insights in an all-inclusive understanding of the impact of HERVs in biology of the host.

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.

scholarly journals Characterization of small RNAs from Ulva prolifera by high-throughput sequencing and bioinformatics analysis

2011 ◽  
Vol 56 (27) ◽  
pp. 2916-2921 ◽  
Author(s):  
AiYou Huang ◽  
GuangCe Wang ◽  
LinWen He ◽  
JianFeng Niu ◽  
BaoYu Zhang
Keyword(s):  
High Throughput ◽  
Small Rnas ◽  
High Throughput Sequencing ◽  
Bioinformatics Analysis ◽  
Ulva Prolifera
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