scholarly journals HBS-Tools for Hairpin Bisulfite Sequencing Data Processing and Analysis

2015 ◽  
Vol 2015 ◽  
pp. 1-4 ◽  
Author(s):  
Ming-an Sun ◽  
Karthik Raja Velmurugan ◽  
David Keimig ◽  
Hehuang Xie
Keyword(s):  
Bisulfite Sequencing ◽  
Reference Genome ◽  
Methylation Pattern ◽  
Global Alignment ◽  
Sequencing Data ◽  
Genome Wide ◽  
Testing Data ◽  
Dna Strands ◽  
Bisulfite Sequencing Data

The emerging genome-wide hairpin bisulfite sequencing (hairpin-BS-Seq) technique enables the determination of the methylation pattern for DNA double strands simultaneously. Compared with traditional bisulfite sequencing (BS-Seq) techniques, hairpin-BS-Seq can determine methylation fidelity and increase mapping efficiency. However, no computational tool has been designed for the analysis of hairpin-BS-Seq data yet. Here we present HBS-tools, a set of command line based tools for the preprocessing, mapping, methylation calling, and summarizing of genome-wide hairpin-BS-Seq data. It accepts paired-end hairpin-BS-Seq reads to recover the original (pre-bisulfite-converted) sequences using global alignment and then calls the methylation statuses for cytosines on both DNA strands after mapping the original sequences to the reference genome. After applying to hairpin-BS-Seq datasets, we found that HBS-tools have a reduced mapping time and improved mapping efficiency compared with state-of-the-art mapping tools. The HBS-tools source scripts, along with user guide and testing data, are freely available for download.

scholarly journals Focal disruption of DNA methylation dynamics at enhancers in IDH-mutant AML cells

Leukemia ◽  
2021 ◽  
Author(s):  
Elisabeth R. Wilson ◽  
Nichole M. Helton ◽  
Sharon E. Heath ◽  
Robert S. Fulton ◽  
Jacqueline E. Payton ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Myeloid Leukemia ◽  
Bisulfite Sequencing ◽  
Sequencing Data ◽  
Genome Wide ◽  
Cd34 Cells ◽  
Recurrent Mutations ◽  
Genome Bisulfite Sequencing ◽  
Bisulfite Sequencing Data ◽  
Acute Myeloid

AbstractRecurrent mutations in IDH1 or IDH2 in acute myeloid leukemia (AML) are associated with increased DNA methylation, but the genome-wide patterns of this hypermethylation phenotype have not been comprehensively studied in AML samples. We analyzed whole-genome bisulfite sequencing data from 15 primary AML samples with IDH1 or IDH2 mutations, which identified ~4000 focal regions that were uniquely hypermethylated in IDHmut samples vs. normal CD34+ cells and other AMLs. These regions had modest hypermethylation in AMLs with biallelic TET2 mutations, and levels of 5-hydroxymethylation that were diminished in IDH and TET-mutant samples, indicating that this hypermethylation results from inhibition of TET-mediated demethylation. Focal hypermethylation in IDHmut AMLs occurred at regions with low methylation in CD34+ cells, implying that DNA methylation and demethylation are active at these loci. AML samples containing IDH and DNMT3AR882 mutations were significantly less hypermethylated, suggesting that IDHmut-associated hypermethylation is mediated by DNMT3A. IDHmut-specific hypermethylation was highly enriched for enhancers that form direct interactions with genes involved in normal hematopoiesis and AML, including MYC and ETV6. These results suggest that focal hypermethylation in IDH-mutant AML occurs by altering the balance between DNA methylation and demethylation, and that disruption of these pathways at enhancers may contribute to AML pathogenesis.

scholarly journals Genome-wide quantitative analysis of DNA methylation from bisulfite sequencing data

2014 ◽  
Vol 30 (13) ◽  
pp. 1933-1934 ◽  
Author(s):  
Kemal Akman ◽  
Thomas Haaf ◽  
Silvia Gravina ◽  
Jan Vijg ◽  
Achim Tresch
Keyword(s):  
Dna Methylation ◽  
Quantitative Analysis ◽  
Bisulfite Sequencing ◽  
Sequencing Data ◽  
Genome Wide ◽  
Bisulfite Sequencing Data

scholarly journals Genome-wide bisulfite sequencing data of normal and Ascosphaera apis-infected larval guts of eastern honeybee

2020 ◽  
Author(s):  
Yu Du ◽  
Zhiwei Zhu ◽  
Huazhi Chen ◽  
Yuanchan Fan ◽  
Jie Wang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Bisulfite Sequencing ◽  
Apis Cerana ◽  
Systematic Investigation ◽  
Regulation Mechanism ◽  
List Type ◽  
Sequencing Data ◽  
Ascosphaera Apis ◽  
Genome Wide ◽  
Bisulfite Sequencing Data

ABSTRACTApis cerana cerana, a subspecies of eastern honey, Apis cerana, plays a specific role in beekeeping industry and ecosystem in China and other Asian countries. Larvae of A. c. cerana can be infected by Ascosphaera apis, the fungal pathogen of chalkbrood. In this article, normal 4-, 5-, and 6-day-old larval guts (AcCK1, AcCK2, AcCK3) and A. apis-infected 4-, 5- and 6-day-old larval guts (AcT1, AcT2, AcT3) of A. c. cerana workers were respectively harvested followed by DNA isolation, bisulfite conversion, cDNA library construction and Illumina sequencing. Based on genome-wide bisulfite sequencing, 79167210, 82175052, 79331489, 81051009, 74742842 and 74849091 raw reads were generated from AcCK1, AcCK2, AcCK3, AcT1, AcT2 and AcT3, and after quality control, 73417030 (92.73%), 76660370 (93.27%), 71804727 (90.44%), 75046507 (92.82%), 67487782 (90.30%) and 67367023 (90.04%) clean reads were obtained, respectively. Additionally, 73333333, 76533333, 71466667, 75066667, 67590965 and 67200000 clean reads were mapped to the reference genome of A. cerana, including 54656767, 58583415, 54127407, 57943220, 52547867 and 51295824 unique mapped clean reads, and 8624392, 8789458, 7531333, 7747337, 6249679 and 5394174 multiple mapped clean reads. The genome-wide bisulfite sequencing data reported here can be used for genome-wide identification of 5mC methylation sites in eastern honeybee larval guts and systematic investigation of DNA methylation-mediated host response to A. apis infection.Value of the dataThe current dataset contributes to genome-wide identification of 5mC methylation sites in normal and A. apis-infected larval guts of eastern honeybee.The reported data could be used for systematic investigation of DNA methylation-mediated response of eastern honeybee larvae to A. apis infection.Our data offers a valuable genetic resource for better understanding epigenetic regulation mechanism involved in eastern honeybee larvae-A. apis interaction.

scholarly journals BiSulfite Bolt: A bisulfite sequencing analysis platform

GigaScience ◽  
2021 ◽  
Vol 10 (5) ◽  
Author(s):  
Colin Farrell ◽  
Michael Thompson ◽  
Anela Tosevska ◽  
Adewale Oyetunde ◽  
Matteo Pellegrini
Keyword(s):  
Data Aggregation ◽  
Bisulfite Sequencing ◽  
Low Complexity ◽  
Sequencing Analysis ◽  
Command Line ◽  
Sequencing Data ◽  
Bisulfite Sequencing Data ◽  
Analysis Platform ◽  
Python Package ◽  
Bisulfite Sequencing Analysis

Abstract Background Bisulfite sequencing is commonly used to measure DNA methylation. Processing bisulfite sequencing data is often challenging owing to the computational demands of mapping a low-complexity, asymmetrical library and the lack of a unified processing toolset to produce an analysis-ready methylation matrix from read alignments. To address these shortcomings, we have developed BiSulfite Bolt (BSBolt), a fast and scalable bisulfite sequencing analysis platform. BSBolt performs a pre-alignment sequencing read assessment step to improve efficiency when handling asymmetrical bisulfite sequencing libraries. Findings We evaluated BSBolt against simulated and real bisulfite sequencing libraries. We found that BSBolt provides accurate and fast bisulfite sequencing alignments and methylation calls. We also compared BSBolt to several existing bisulfite alignment tools and found BSBolt outperforms Bismark, BSSeeker2, BISCUIT, and BWA-Meth based on alignment accuracy and methylation calling accuracy. Conclusion BSBolt offers streamlined processing of bisulfite sequencing data through an integrated toolset that offers support for simulation, alignment, methylation calling, and data aggregation. BSBolt is implemented as a Python package and command line utility for flexibility when building informatics pipelines. BSBolt is available at https://github.com/NuttyLogic/BSBolt under an MIT license.

scholarly journals GBSA: a comprehensive software for analysing whole genome bisulfite sequencing data

2012 ◽  
Vol 41 (4) ◽  
pp. e55-e55 ◽  
Author(s):  
Touati Benoukraf ◽  
Sarawut Wongphayak ◽  
Luqman Hakim Abdul Hadi ◽  
Mengchu Wu ◽  
Richie Soong
Keyword(s):  
Bisulfite Sequencing ◽  
Whole Genome ◽  
Sequencing Data ◽  
Whole Genome Bisulfite Sequencing ◽  
Genome Bisulfite Sequencing ◽  
Bisulfite Sequencing Data

scholarly journals MethGo: a comprehensive tool for analyzing whole-genome bisulfite sequencing data

BMC Genomics ◽  
2015 ◽  
Vol 16 (Suppl 12) ◽  
pp. S11 ◽  
Author(s):  
Wen-Wei Liao ◽  
Ming-Ren Yen ◽  
Evaline Ju ◽  
Fei-Man Hsu ◽  
Larry Lam ◽  
...  
Keyword(s):  
Bisulfite Sequencing ◽  
Whole Genome ◽  
Sequencing Data ◽  
Whole Genome Bisulfite Sequencing ◽  
Genome Bisulfite Sequencing ◽  
Bisulfite Sequencing Data
Sign in / Sign up

Export Citation Format

Share Document