Evaluation of TagSeq, a reliable low-cost alternative for RNAseq

Molecular Ecology Resources

Volumn 16, Issue 6, 2016, Pages 1315-1321

  Lohman, Brian K ^a   Weber, Jesse N ^a,b   Bolnick, Daniel I ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b UNIVERSITY OF MONTANA   (United States)

Author keywords

3'Tag based sequencing; ecological genetics; RNAseq

Indexed keywords

BIOLOGY; COST; ECONOMICS; GENE EXPRESSION PROFILING; HIGH THROUGHPUT SEQUENCING; PROCEDURES;

COMPUTATIONAL BIOLOGY; COSTS AND COST ANALYSIS; GENE EXPRESSION PROFILING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING;

EID: 84991373468     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12529     Document Type: Article

References (20)

1. Aird D, Ross MG, Chen WS et al. (2011) Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biology, 12, R18.
2. Barribeau SM, Sadd BM, du Plessis L, Schmid-Hempel P (2014) Gene expression differences underlying genotype-by-genotype specificty in a host-parasite system. Proceeding of the National Academy of Sciences, 111, 3496–3501.
3. Des Marais DL, Skillern WD, Juenger TE (2015) Deeply diverged alleles in the Arabidopsis AREB1 transcription factor drive genome-wide differences in transcriptional response to the environment. Molecular Biology and Evolution, 32, 956–969.
4. Dixon GB, Davies SW, Aglyamova GA, Meyer E, Bay LK, Matz MV (2015) Genomic determinants of coral heat tolerance across latitudes. Science, 348, 1460–1462.
5. Foth BJ, Tsai IJ, Reid AJ et al. (2014) Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction. Nature Genetics, 46, 693–700.
6. Lenz TL, Eizaguirre C, Rotter B, Kalbe M, Milinski M (2013) Exploring local immunological adaptation of two stickleback ecotypes by experimental infection and transcriptome-wide digital gene expression analysis. Molecular Ecology, 22, 774–786.
7. Li H, Durbin R (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics, 26, 589–595.
8. Lovell JT, Mullen JL, Lowry DB et al. (2015) Exploiting differential gene expression and epistasis to discover candidate genes for drought-associated QTLs in Arabidopsis thaliana. The Plant Cell, 27, 969–983.
9. Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet Journal, 17, 10–12.
10. Meyer E, Aglyamova GV, Matz MV (2011) Profiling gene expression responses of coral larvae (Acropora millepora) to elevated temperature and settlement inducers using a novel RNA-Seq procedure. Molecular Ecology, 20, 3599–3616.
11. Pickrell JK, Marioni JC, Pai AA et al. (2010) Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature, 464, 768–772.
12. Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26, 841–842.
13. R Development Core Team (2007) R: a language and environment for statistical computing. R Foundation for Statistical Computing: Vienna, Austria.
14. Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L (2011) Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biology, 12, R22.
15. Rohland N, Reich D (2012) Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture. Genome Research, 22, 939–946.
16. Schweyen H, Rozenberg A, Leese F (2014) Detection and removal of PCR duplicates in population genomic ddRAD studies by addition of a degenerate base region (DBR) in sequencing adapters. The Biological Bulletin, 227, 146–160.
17. The ENCODE Consortium (2011) Standards, Guidelines, and Best Practices for RNA-seq. Available from: https://genome.ucsc.edu/ENCODE/protocols/dataStandards/ENCODE_RNAseq_Standards_V1.0.pdf.
18. Todd EV, Black MA, Gemmell NJ (2016) The power and promise of RNA-seq in ecology and evolution. Molecular Ecology, 25, 1224–1241.
19. Trapnell C, Williams BA, Pertea G et al. (2010) Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology, 28, 511.
20. Videvall E, Cornwallis CK, Palinauskas V, Valkiūnas G, Hellgren O (2015) The avian transcriptome response to malaria infection. Molecular Biology and Evolution, 32, 1255–1267.