scholarly journals Evaluation and Adaptation of a Laboratory-Based cDNA Library Preparation Protocol for Retrospective Sequencing of Archived MicroRNAs from up to 35-Year-Old Clinical FFPE Specimens

2017 ◽  
Vol 18 (3) ◽  
pp. 627 ◽  
Author(s):  
Olivier Loudig ◽  
Tao Wang ◽  
Kenny Ye ◽  
Juan Lin ◽  
Yihong Wang ◽  
...  
Keyword(s):  
Cdna Library ◽  
Library Preparation ◽  
Cdna Library Preparation ◽  
Library Preparation Protocol

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.

High Throughput Semi-Automated SARS-CoV-2 Library Preparation Protocol for Ion Torrent Sequencing using Opentrons, New England Biolabs Kit, and ARTIC Primers v2

protocols.io ◽  
2021 ◽  
Author(s):  
Elias Dahdouh ◽  
Fernando Lázaro Perona ◽  
María Rodríguez Tejedor ◽  
Rubén Cáceres Sánchez ◽  
Iván Bloise Sánchez ◽  
...  
Keyword(s):  
New England ◽  
High Throughput ◽  
Ion Torrent ◽  
Library Preparation ◽  
England Biolabs ◽  
Ion Torrent Sequencing ◽  
Library Preparation Protocol
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