An automated method for efficient, accurate and reproducible construction of RNA-seq libraries Genomics

BMC Research Notes

Volumn 8, Issue 1, 2015, Pages

  Tsompana, Maria ^a   Valiyaparambil, Sujith ^a   Bard, Jonathan ^a   Marzullo, Brandon ^a   Nowak, Norma ^a   Buck, Michael Joseph ^a  

^a UNIVERSITY AT BUFFALO   (United States)

Author keywords

Chromatin; Epigenetics; Next generation sequencing; RNA seq; Transcription

Indexed keywords

TRANSCRIPTOME;

ANIMAL; DEVICES; GENE EXPRESSION PROFILING; GENE LIBRARY; GENOME; HIGH THROUGHPUT SEQUENCING; LABORATORY AUTOMATION; MOUSE; PROCEDURES; SEQUENCE ANALYSIS; STATISTICS AND NUMERICAL DATA;

ANIMALS; AUTOMATION, LABORATORY; GENE EXPRESSION PROFILING; GENE LIBRARY; GENOME; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICE; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME;

EID: 84926670353     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/s13104-015-1089-9     Document Type: Article

References (7)

1. Consortium EP. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science. 2004;306(5696):636-40.
2. Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, et al. The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol. 2010;28(10):1045-8.
3. Chadwick LRNA-SEQ. The NIH roadmap epigenomics program data resource. Epigenomics. 2012;4(3):317-24.
4. Celniker SE, Dillon LA, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, et al. Unlocking the secrets of the genome. Nature. 2009;459(7249):927-30.
5. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14(4):R36.
6. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28(5):511-5.
7. Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012;7(3):562-78.