Abstract 5409: Assessment of the MammaPrint 70-gene profile using RNA sequencing technology

Author(s):  
Lorenza Mittempergher ◽  
Jacob B. Spangler ◽  
Mireille H. Snel ◽  
Leonie J. Delahaye ◽  
Iris de Rink ◽  
...  
Author(s):  
Paul L. Auer ◽  
Rebecca W Doerge

RNA sequencing technology is providing data of unprecedented throughput, resolution, and accuracy. Although there are many different computational tools for processing these data, there are a limited number of statistical methods for analyzing them, and even fewer that acknowledge the unique nature of individual gene transcription. We introduce a simple and powerful statistical approach, based on a two-stage Poisson model, for modeling RNA sequencing data and testing for biologically important changes in gene expression. The advantages of this approach are demonstrated through simulations and real data applications.


2015 ◽  
Vol 21 (3) ◽  
Author(s):  
Ian C. Clift

The regenerative medicine space is one that is set to explode with considerable innovation and profitability for shrewd biotechnologists. I had the opportunity to speak with Michael West, PhD., CEO of BioTime (BTX) and found a man passionate about regenerative medicine and of course passionate about his role in its future. In this conversation I learned of West's vision, which I think provides some powerful clues as to areas of future growth in the biotech sector. He points to three scientific advances that make this vision actualizable. First, sequencing technology that allows us to perform RNA sequencing for around 300 dollars or less, second the common and reversible molecular basis for age-related diseases, and finally industrial scaling of pure cell lines like the ones manufactured by BTX. Let's look at the three enabling technologies that West touched on and examine how they are being utilized to achieve West's vision within BTX and others involved in the anti-aging revolution.


2016 ◽  
Vol 13 (5) ◽  
Author(s):  
Matthew Kanke ◽  
Jeanette Baran-Gale ◽  
Jonathan Villanueva ◽  
Praveen Sethupathy

SummarySmall non-coding RNAs, in particular microRNAs, are critical for normal physiology and are candidate biomarkers, regulators, and therapeutic targets for a wide variety of diseases. There is an ever-growing interest in the comprehensive and accurate annotation of microRNAs across diverse cell types, conditions, species, and disease states. Highthroughput sequencing technology has emerged as the method of choice for profiling microRNAs. Specialized bioinformatic strategies are required to mine as much meaningful information as possible from the sequencing data to provide a comprehensive view of the microRNA landscape. Here we present miRquant 2.0, an expanded bioinformatics tool for accurate annotation and quantification of microRNAs and their isoforms (termed isomiRs) from small RNA-sequencing data. We anticipate that miRquant 2.0 will be useful for researchers interested not only in quantifying known microRNAs but also mining the rich well of additional information embedded in small RNA-sequencing data.


2013 ◽  
Author(s):  
Jeanette Baran-Gale ◽  
Michael R Erdos ◽  
Christina Sison ◽  
Alice Young ◽  
Emily E Fannin ◽  
...  

Recent advances in sequencing technology have helped unveil the unexpected complexity and diversity of small RNAs. A critical step in small RNA library preparation for sequencing is the ligation of adapter sequences to both the 5’ and 3’ ends of small RNAs. Two widely used protocols for small RNA library preparation, Illumina v1.5 and Illumina TruSeq, use different pairs of adapter sequences. In this study, we compare the results of small RNA-sequencing between v1.5 and TruSeq and observe a striking differential bias. Nearly 100 highly expressed microRNAs (miRNAs) are >5-fold differentially detected and 48 miRNAs are >10-fold differentially detected between the two methods of library preparation. In fact, some miRNAs, such as miR-24-3p, are over 30-fold differentially detected. The results are reproducible across different sequencing centers (NIH and UNC) and both major Illumina sequencing platforms, GAIIx and HiSeq. While some level of bias in library preparation is not surprising, the apparent massive differential bias between these two widely used adapter sets is not well appreciated. As increasingly more laboratories transition to the newer TruSeq-based library preparation for small RNAs, researchers should be aware of the extent to which the results may differ from previously published results using v1.5.


2021 ◽  
Vol 0 (0) ◽  
pp. 0-0
Author(s):  
Lian He ◽  
Anjing Lu ◽  
Lin Qin ◽  
Qianru Zhang ◽  
Hua Ling ◽  
...  

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Abbas Jariani ◽  
Lieselotte Vermeersch ◽  
Bram Cerulus ◽  
Gemma Perez-Samper ◽  
Karin Voordeckers ◽  
...  

Current methods for single-cell RNA sequencing (scRNA-seq) of yeast cells do not match the throughput and relative simplicity of the state-of-the-art techniques that are available for mammalian cells. In this study, we report how 10x Genomics’ droplet-based single-cell RNA sequencing technology can be modified to allow analysis of yeast cells. The protocol, which is based on in-droplet spheroplasting of the cells, yields an order-of-magnitude higher throughput in comparison to existing methods. After extensive validation of the method, we demonstrate its use by studying the dynamics of the response of isogenic yeast populations to a shift in carbon source, revealing the heterogeneity and underlying molecular processes during this shift. The method we describe opens new avenues for studies focusing on yeast cells, as well as other cells with a degradable cell wall.


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