cDNA Library Preparation

2013 ◽  
pp. 29-40
Author(s):  
Maarten Kooiker ◽  
Gang-Ping Xue
Keyword(s):  
Cdna Library ◽  
Library Preparation ◽  
Cdna Library Preparation

scholarly journals Barcoded cDNA library preparation for small RNA profiling by next-generation sequencing

Methods ◽  
2012 ◽  
Vol 58 (2) ◽  
pp. 164-170 ◽  
Author(s):  
Markus Hafner ◽  
Neil Renwick ◽  
Thalia A. Farazi ◽  
Aleksandra Mihailović ◽  
John T.G. Pena ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Cdna Library ◽  
Small Rna ◽  
Library Preparation ◽  
Next Generation ◽  
Rna Profiling ◽  
Generation Sequencing ◽  
Cdna Library Preparation

scholarly journals An improved iCLIP protocol

2021 ◽  
Author(s):  
Flora C. Y. Lee ◽  
Anob M. Chakrabarti ◽  
Heike Hänel ◽  
Elisa Monzón-Casanova ◽  
Martina Hallegger ◽  
...  
Keyword(s):  
Cdna Library ◽  
Binding Sites ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Library Preparation ◽  
Powerful Technique ◽  
Uv Crosslinking ◽  
Nucleotide Resolution ◽  
Cdna Library Preparation

AbstractCrosslinking and Immunoprecipitation (CLIP) is a powerful technique to obtain transcriptome-wide maps of in vivo protein-RNA interactions, which are important to understand the post-transcriptional mechanisms mediated by RNA binding proteins (RBPs). Many variant CLIP protocols have been developed to improve the efficiency and convenience of cDNA library preparation. Here we describe an improved individual nucleotide resolution CLIP protocol (iiCLIP), which can be completed within 4 days from UV crosslinking to libraries for sequencing. For benchmarking, we directly compared PTBP1 iiCLIP libraries with the iCLIP2 protocol produced under standardised conditions, and with public eCLIP and iCLIP PTBP1 data. We visualised enriched motifs surrounding the identified crosslink positions and RNA maps of these crosslinks around the alternative exons regulated by PTBP1. Notably, motif enrichment was higher in iiCLIP and iCLIP2 in comparison to public eCLIP and iCLIP, and we show how this impacts the specificity of RNA maps. In conclusion, iiCLIP is technically convenient and efficient, and enables production of highly specific datasets for identifying RBP binding sites.

scholarly journals Nanopore native RNA sequencing of a human poly(A) transcriptome: RNA extraction, cDNA conversion and direct RNA and cDNA library preparation for Oxford Nanopore

2019 ◽  
Author(s):  
Rachael E. Workman ◽  
Alison D. Tang ◽  
Paul S. Tang ◽  
Miten Jain ◽  
John R. Tyson ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Rna Extraction ◽  
Human Cell Line ◽  
Cdna Libraries ◽  
Library Preparation ◽  
Sequencing Technologies ◽  
Oxford Nanopore ◽  
Sequencing Strategy ◽  
Oxford Nanopore Technologies ◽  
Cdna Library Preparation

Abstract High throughput cDNA sequencing technologies have dramatically advanced our understanding of transcriptome complexity and regulation. However, these methods lose information contained in biological RNA because the copied reads are often short and because modifications are not carried forward in cDNA. We address these limitations using a native poly(A) RNA sequencing strategy developed by Oxford Nanopore Technologies (ONT). Our study focused on poly(A) RNA from the human cell line GM12878, generating 9.9 million aligned sequence reads. These native RNA reads had an aligned N50 length of 1294 bases, and a maximum aligned length of over 21,000 bases. A total of 78,199 high-confidence isoforms were identified by combining long nanopore reads with short higher accuracy Illumina reads. We describe methods for extracting intact RNA, poly-A selection, cDNA conversion for a portion of sample, and library preparation for both direct RNA and cDNA libraries.

scholarly journals GENE EXPRESSION AND SEQUENCING TECHNIQUES OF TRANSCRIPTOME TO ELUCIDATE NOVEL FUNCTION FOR PHOSPHOLIPASE (S) ENZYME

2018 ◽  
Vol 7 (5) ◽  
Author(s):  
M G Tyagi, S Saha, D Mukherjee, A Ramaswamy, PA Vora
Keyword(s):  
Gene Expression ◽  
Phospholipase D ◽  
Review Article ◽  
Library Preparation ◽  
Rna Seq ◽  
Clinical Therapeutics ◽  
Functional Roles ◽  
Rna Biogenesis ◽  
Fusion Detection ◽  
Cdna Library Preparation

Sequencing of RNA, or RNA-Seq, is now a common method to analyze gene expression and to uncover novel RNA species. Aspects of RNA biogenesis and metabolism can be evaluated with specialized methods for cDNA library preparation. In this study, the review examines current RNA-Seq methods for general analysis of gene expression and several specific applications, including isoform and gene fusion detection, targeted sequencing and single-cell analysis.Elucidating the transcriptome may help in better understanding of phospholipase function and novel application in diagnostics and clinical therapeutics. Therefore this review article focusses on the transcriptome analysis of the phospholipase enzymes i.e phospholipase A2, D and C isozymes and characterizing their functional roles in specialized disorders or for therapy. Key words:   RNA, sequencing, transcriptome, phospholipase D, gene, expression

Analysis of cDNA library of Cucumis sativus L. challenged by Pseudomonas syringae pv. Lachrymans

2009 ◽  
Vol 31 (10) ◽  
pp. 1042-1048
Author(s):  
Guan-Jun LIU ◽  
Li-Juan WANG ◽  
Zhi-Wei QIN ◽  
Ling-Bo MENG
Keyword(s):  
Cdna Library ◽  
Cucumis Sativus ◽  
Pseudomonas Syringae
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