scholarly journals High concordance between Illumina HiSeq2500 and NextSeq500 for reduced representation bisulfite sequencing (RRBS)

Genomics Data ◽  
2016 ◽  
Vol 10 ◽  
pp. 97-100 ◽  
Author(s):  
Danqing Yin ◽  
Matthew E. Ritchie ◽  
Jafar S. Jabbari ◽  
Tamara Beck ◽  
Marnie E. Blewitt ◽  
...  
Keyword(s):  
Bisulfite Sequencing ◽  
Reduced Representation ◽  
Reduced Representation Bisulfite Sequencing ◽  
High Concordance

scholarly journals Technical Considerations for Reduced Representation Bisulfite Sequencing with Multiplexed Libraries

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Aniruddha Chatterjee ◽  
Euan J. Rodger ◽  
Peter A. Stockwell ◽  
Robert J. Weeks ◽  
Ian M. Morison
Keyword(s):  
Bisulfite Sequencing ◽  
Flow Cell ◽  
Throughput Capacity ◽  
Sequencing Data ◽  
Bioinformatics Pipeline ◽  
Illumina Hiseq ◽  
Reduced Representation ◽  
Reduced Representation Bisulfite Sequencing ◽  
Unique Mapping ◽  
Nucleotide Resolution

Reduced representation bisulfite sequencing (RRBS), which couples bisulfite conversion and next generation sequencing, is an innovative method that specifically enriches genomic regions with a high density of potential methylation sites and enables investigation of DNA methylation at single-nucleotide resolution. Recent advances in the Illumina DNA sample preparation protocol and sequencing technology have vastly improved sequencing throughput capacity. Although the new Illumina technology is now widely used, the unique challenges associated with multiplexed RRBS libraries on this platform have not been previously described. We have made modifications to the RRBS library preparation protocol to sequence multiplexed libraries on a single flow cell lane of the Illumina HiSeq 2000. Furthermore, our analysis incorporates a bioinformatics pipeline specifically designed to process bisulfite-converted sequencing reads and evaluate the output and quality of the sequencing data generated from the multiplexed libraries. We obtained an average of 42 million paired-end reads per sample for each flow-cell lane, with a high unique mapping efficiency to the reference human genome. Here we provide a roadmap of modifications, strategies, and trouble shooting approaches we implemented to optimize sequencing of multiplexed libraries on an a RRBS background.

Application of multiplexed reduced representation bisulfite sequencing (mRRBS) to environmental epigenetic studies: comparison to the 450K Illumina BeadChip

2013 ◽  
Vol 2013 (1) ◽  
pp. 5363
Author(s):  
Benedetta Izzi ◽  
Juan J. Carmona ◽  
Alexandra M. Binder ◽  
Allan C. Just ◽  
Jitendra Barupal ◽  
...  
Keyword(s):  
Bisulfite Sequencing ◽  
Reduced Representation ◽  
Reduced Representation Bisulfite Sequencing

scholarly journals A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing: Fig. 1.

2015 ◽  
Vol 31 (12) ◽  
pp. 2040-2042 ◽  
Author(s):  
Xuefeng Wang ◽  
Xiaoqing Yu ◽  
Wei Zhu ◽  
W. Richard McCombie ◽  
Eric Antoniou ◽  
...  
Keyword(s):  
Bisulfite Sequencing ◽  
Reduced Representation ◽  
Reduced Representation Bisulfite Sequencing

Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling

2011 ◽  
Vol 6 (4) ◽  
pp. 468-481 ◽  
Author(s):  
Hongcang Gu ◽  
Zachary D Smith ◽  
Christoph Bock ◽  
Patrick Boyle ◽  
Andreas Gnirke ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Bisulfite Sequencing ◽  
Reduced Representation ◽  
Reduced Representation Bisulfite Sequencing ◽  
Dna Methylation Profiling ◽  
Genome Scale ◽  
Methylation Profiling
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