RT Journal Article
SR Electronic
T1 Dumpster diving in RNA-sequencing to find the source of every last read
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 053041
DO 10.1101/053041
A1 Serghei Mangul
A1 Harry Taegyun Yang
A1 Nicolas Strauli
A1 Franziska Gruhl
A1 Timothy Daley
A1 Stephanie Christenson
A1 Agata Wesolowska-Andersen
A1 Roberto Spreafico
A1 Cydney Rios
A1 Celeste Eng
A1 Andrew D. Smith
A1 Ryan D. Hernandez
A1 Roel A. Ophoff
A1 Jose Rodriguez Santana
A1 Prescott G. Woodruff
A1 Esteban Burchard
A1 Max A. Seibold
A1 Sagiv Shifman
A1 Eleazar Eskin
A1 Noah Zaitlen
YR 2016
UL http://biorxiv.org/content/early/2016/05/13/053041.abstract
AB 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 gene expression, and disease etiology.The ROP pipeline is freely available at https://sergheimangul.wordpress.com/rop/