Methods (San Diego, Calif.), 2013-09, Vol.63 (2), p.126-134
- Miller, David F.B.
- Yan, Pearlly S.
- Buechlein, Aaron
- Rodriguez, Benjamin A.
- Yilmaz, Ayse S.
- Goel, Shokhi
- Lin, Hai
- Collins-Burow, Bridgette
- Rhodes, Lyndsay V.
- Braun, Chris
- Pradeep, Sunila
- Rupaimoole, Rajesha
- Dalkilic, Mehmet
- Sood, Anil K.
- Burow, Matthew E.
- Tang, Haixu
- Huang, Tim H.
- Liu, Yunlong
- Rusch, Douglas B.
- Nephew, Kenneth P.
2013
Details
- Autor(en) / Beteiligte
- Miller, David F.B.
- Yan, Pearlly S.
- Buechlein, Aaron
- Rodriguez, Benjamin A.
- Yilmaz, Ayse S.
- Goel, Shokhi
- Lin, Hai
- Collins-Burow, Bridgette
- Rhodes, Lyndsay V.
- Braun, Chris
- Pradeep, Sunila
- Rupaimoole, Rajesha
- Dalkilic, Mehmet
- Sood, Anil K.
- Burow, Matthew E.
- Tang, Haixu
- Huang, Tim H.
- Liu, Yunlong
- Rusch, Douglas B.
- Nephew, Kenneth P.
- Titel
- A new method for stranded whole transcriptome RNA-seq
- Ist Teil von
- Methods (San Diego, Calif.), 2013-09, Vol.63 (2), p.126-134
- Ort / Verlag
- United States: Elsevier Inc
- Erscheinungsjahr
- 2013
- Link zum Volltext
- Quelle
- Access via ScienceDirect (Elsevier)
- Beschreibungen/Notizen
- This report describes an improved protocol to generate stranded, barcoded RNA-seq libraries to capture the whole transcriptome. By optimizing the use of duplex specific nuclease (DSN) to remove ribosomal RNA reads from stranded barcoded libraries, we demonstrate improved efficiency of multiplexed next generation sequencing (NGS). This approach detects expression profiles of all RNA types, including miRNA (microRNA), piRNA (Piwi-interacting RNA), snoRNA (small nucleolar RNA), lincRNA (long non-coding RNA), mtRNA (mitochondrial RNA) and mRNA (messenger RNA) without the use of gel electrophoresis. The improved protocol generates high quality data that can be used to identify differential expression in known and novel coding and non-coding transcripts, splice variants, mitochondrial genes and SNPs (single nucleotide polymorphisms).
- Sprache
- Englisch
- Identifikatoren
- ISSN: 1046-2023eISSN: 1095-9130DOI: 10.1016/j.ymeth.2013.03.023Titel-ID: cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_3739992
- Format
- –
- Schlagworte
- Cell Line, Tumor, Duplex-specific nuclease, Gene expression, Gene Expression Profiling - methods, Gene Library, High-Throughput Nucleotide Sequencing, Humans, Molecular Sequence Annotation, Polymorphism, Single Nucleotide, Protein Isoforms - genetics, Protein Isoforms - metabolism, Real-Time Polymerase Chain Reaction, Reverse Transcriptase Polymerase Chain Reaction, Ribonucleases - chemistry, RNA, Messenger - genetics, RNA, Messenger - isolation & purification, RNA, Messenger - metabolism, RNA, Ribosomal - chemistry, RNA, Ribosomal - isolation & purification, RNA-seq, Sequence Analysis, RNA, Transcriptome