May 13, 2016

Dumpster diving in RNA-sequencing to find the source of every last read

BioRxiv : the Preprint Server for Biology
Serghei MangulEsteban Burchard

Abstract

High throughput RNA sequencing technologies have provided invaluable research opportunities across distinct scientific domains by producing quantitative readouts of the transcriptional activity of both entire cellular populations and single cells. The majority of RNA-Seq analyses begin by mapping each experimentally produced sequence (i.e., read) to a set of annotated reference sequences for the organism of interest. For both biological and technical reasons, a significant fraction of reads remains unmapped. In this work we develop a read origin protocol (ROP) aimed at discovering the source of all reads, originated from complex RNA molecules, recombinant antibodies and microbial communities. Our approach can account for 98.8% of all reads across poly(A) and ribo-depletion protocols. Furthermore, using ROP we show that immune profiles of asthmatic individuals are significantly different from the control individuals with decreased average per sample T-cell/B-cell receptor diversity and that immune diversity is inversely correlated with microbial load. This demonstrates the potential of ROP to exploit unmapped reads to better understand the functional mechanisms underlying the connection between immune system, microbiome, human g...Continue Reading

  • References
  • Citations

References

  • We're still populating references for this paper, please check back later.
  • References
  • Citations

Citations

  • This paper may not have been cited yet.

Mentioned in this Paper

Immune System
T-Lymphocyte
Receptors, Antigen, B-Cell
Sequence Determinations, RNA
Research Opportunity
Transcription, Genetic
ROP chemical
Etiology
Gene Expression
Poly A

About this Paper

Related Feeds

American Thoracic Society: Clinical Problems

This feed has been developed in conjunction with the American Thoracic Society for the benefit of its Clinical Problems Assembly. It highlights new and impactful papers on clinical therapeutics, diagnoses, and practices pertaining to respiratory disease.

Asthma (Preprints)

Asthma is a condition in which your airways narrow and swell. This can make breathing difficult and trigger coughing, wheezing and shortness of breath. Discover the latest preprints here.

Allergy and Asthma

Allergy and asthma are inflammatory disorders that are triggered by the activation of an allergen-specific regulatory t cell. These t cells become activated when allergens are recognized by allergen-presenting cells. Here is the latest research on allergy and asthma.

BioRxiv & MedRxiv Preprints

BioRxiv and MedRxiv are the preprint servers for biology and health sciences respectively, operated by Cold Spring Harbor Laboratory. Here are the latest preprint articles (which are not peer-reviewed) from BioRxiv and MedRxiv.

B cells: Gene Expression

B lymphocytes are white blood cells that play a role in the adaptive immune system by secreting antibodies. Here is the latest research on gene expression in B cells.

Asthma

This feed focuses in Asthma in which your airways narrow and swell. This can make breathing difficult and trigger coughing, wheezing and shortness of breath.