ROP

Dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues

Serghei Mangul, Harry Taegyun Yang, Nicolas Strauli, Franziska Gruhl, Hagit T. Porath, Kevin Hsieh, Linus Chen, Timothy Daley, Stephanie Christenson, Agata Wesolowska-Andersen, Roberto Spreafico, Cydney Rios, Celeste Eng, Andrew D. Smith, Ryan D. Hernandez, Roel A. Ophoff, Jose Rodriguez Santana, Erez Y. Levanon, Prescott G. Woodruff, Esteban Burchard & 4 others Max A. Seibold, Sagiv Shifman, Eleazar Eskin, Noah Zaitlen

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

High-throughput RNA-sequencing (RNA-seq) technologies provide an unprecedented opportunity to explore the individual transcriptome. Unmapped reads are a large and often overlooked output of standard RNA-seq analyses. Here, we present Read Origin Protocol (ROP), a tool for discovering the source of all reads originating from complex RNA molecules. We apply ROP to samples across 2630 individuals from 54 diverse human tissues. Our approach can account for 99.9% of 1 trillion reads of various read length. Additionally, we use ROP to investigate the functional mechanisms underlying connections between the immune system, microbiome, and disease. ROP is freely available at https://github.com/smangul1/rop/wiki.

Original languageEnglish (US)
Article number36
JournalGenome biology
Volume19
Issue number1
DOIs
StatePublished - Feb 15 2018

Fingerprint

RNA Sequence Analysis
Diving
diving
RNA
sequence analysis
High-Throughput Nucleotide Sequencing
Microbiota
Immune System Diseases
Transcriptome
transcriptome
immune system
Technology
tissue
protocol
tissues
sampling

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

Cite this

Mangul, S., Yang, H. T., Strauli, N., Gruhl, F., Porath, H. T., Hsieh, K., ... Zaitlen, N. (2018). ROP: Dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues. Genome biology, 19(1), [36]. https://doi.org/10.1186/s13059-018-1403-7
Mangul, Serghei ; Yang, Harry Taegyun ; Strauli, Nicolas ; Gruhl, Franziska ; Porath, Hagit T. ; Hsieh, Kevin ; Chen, Linus ; Daley, Timothy ; Christenson, Stephanie ; Wesolowska-Andersen, Agata ; Spreafico, Roberto ; Rios, Cydney ; Eng, Celeste ; Smith, Andrew D. ; Hernandez, Ryan D. ; Ophoff, Roel A. ; Santana, Jose Rodriguez ; Levanon, Erez Y. ; Woodruff, Prescott G. ; Burchard, Esteban ; Seibold, Max A. ; Shifman, Sagiv ; Eskin, Eleazar ; Zaitlen, Noah. / ROP : Dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues. In: Genome biology. 2018 ; Vol. 19, No. 1.
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title = "ROP: Dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues",
abstract = "High-throughput RNA-sequencing (RNA-seq) technologies provide an unprecedented opportunity to explore the individual transcriptome. Unmapped reads are a large and often overlooked output of standard RNA-seq analyses. Here, we present Read Origin Protocol (ROP), a tool for discovering the source of all reads originating from complex RNA molecules. We apply ROP to samples across 2630 individuals from 54 diverse human tissues. Our approach can account for 99.9{\%} of 1 trillion reads of various read length. Additionally, we use ROP to investigate the functional mechanisms underlying connections between the immune system, microbiome, and disease. ROP is freely available at https://github.com/smangul1/rop/wiki.",
author = "Serghei Mangul and Yang, {Harry Taegyun} and Nicolas Strauli and Franziska Gruhl and Porath, {Hagit T.} and Kevin Hsieh and Linus Chen and Timothy Daley and Stephanie Christenson and Agata Wesolowska-Andersen and Roberto Spreafico and Cydney Rios and Celeste Eng and Smith, {Andrew D.} and Hernandez, {Ryan D.} and Ophoff, {Roel A.} and Santana, {Jose Rodriguez} and Levanon, {Erez Y.} and Woodruff, {Prescott G.} and Esteban Burchard and Seibold, {Max A.} and Sagiv Shifman and Eleazar Eskin and Noah Zaitlen",
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Mangul, S, Yang, HT, Strauli, N, Gruhl, F, Porath, HT, Hsieh, K, Chen, L, Daley, T, Christenson, S, Wesolowska-Andersen, A, Spreafico, R, Rios, C, Eng, C, Smith, AD, Hernandez, RD, Ophoff, RA, Santana, JR, Levanon, EY, Woodruff, PG, Burchard, E, Seibold, MA, Shifman, S, Eskin, E & Zaitlen, N 2018, 'ROP: Dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues', Genome biology, vol. 19, no. 1, 36. https://doi.org/10.1186/s13059-018-1403-7

ROP : Dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues. / Mangul, Serghei; Yang, Harry Taegyun; Strauli, Nicolas; Gruhl, Franziska; Porath, Hagit T.; Hsieh, Kevin; Chen, Linus; Daley, Timothy; Christenson, Stephanie; Wesolowska-Andersen, Agata; Spreafico, Roberto; Rios, Cydney; Eng, Celeste; Smith, Andrew D.; Hernandez, Ryan D.; Ophoff, Roel A.; Santana, Jose Rodriguez; Levanon, Erez Y.; Woodruff, Prescott G.; Burchard, Esteban; Seibold, Max A.; Shifman, Sagiv; Eskin, Eleazar; Zaitlen, Noah.

In: Genome biology, Vol. 19, No. 1, 36, 15.02.2018.

Research output: Contribution to journalArticle

TY - JOUR

T1 - ROP

T2 - Dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues

AU - Mangul, Serghei

AU - Yang, Harry Taegyun

AU - Strauli, Nicolas

AU - Gruhl, Franziska

AU - Porath, Hagit T.

AU - Hsieh, Kevin

AU - Chen, Linus

AU - Daley, Timothy

AU - Christenson, Stephanie

AU - Wesolowska-Andersen, Agata

AU - Spreafico, Roberto

AU - Rios, Cydney

AU - Eng, Celeste

AU - Smith, Andrew D.

AU - Hernandez, Ryan D.

AU - Ophoff, Roel A.

AU - Santana, Jose Rodriguez

AU - Levanon, Erez Y.

AU - Woodruff, Prescott G.

AU - Burchard, Esteban

AU - Seibold, Max A.

AU - Shifman, Sagiv

AU - Eskin, Eleazar

AU - Zaitlen, Noah

PY - 2018/2/15

Y1 - 2018/2/15

N2 - High-throughput RNA-sequencing (RNA-seq) technologies provide an unprecedented opportunity to explore the individual transcriptome. Unmapped reads are a large and often overlooked output of standard RNA-seq analyses. Here, we present Read Origin Protocol (ROP), a tool for discovering the source of all reads originating from complex RNA molecules. We apply ROP to samples across 2630 individuals from 54 diverse human tissues. Our approach can account for 99.9% of 1 trillion reads of various read length. Additionally, we use ROP to investigate the functional mechanisms underlying connections between the immune system, microbiome, and disease. ROP is freely available at https://github.com/smangul1/rop/wiki.

AB - High-throughput RNA-sequencing (RNA-seq) technologies provide an unprecedented opportunity to explore the individual transcriptome. Unmapped reads are a large and often overlooked output of standard RNA-seq analyses. Here, we present Read Origin Protocol (ROP), a tool for discovering the source of all reads originating from complex RNA molecules. We apply ROP to samples across 2630 individuals from 54 diverse human tissues. Our approach can account for 99.9% of 1 trillion reads of various read length. Additionally, we use ROP to investigate the functional mechanisms underlying connections between the immune system, microbiome, and disease. ROP is freely available at https://github.com/smangul1/rop/wiki.

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U2 - 10.1186/s13059-018-1403-7

DO - 10.1186/s13059-018-1403-7

M3 - Article

VL - 19

JO - Genome Biology

JF - Genome Biology

SN - 1474-7596

IS - 1

M1 - 36

ER -