scholarly journals Generation of High Quality Chromatin Immunoprecipitation DNA Template for High-throughput Sequencing (ChIP-seq)

10.3791/50286 ◽  
2013 ◽  
Author(s):  
Sandra Deliard ◽  
Jianhua Zhao ◽  
Qianghua Xia ◽  
Struan F.A. Grant
Keyword(s):  
High Throughput ◽  
Chromatin Immunoprecipitation ◽  
High Throughput Sequencing ◽  
High Quality ◽  
Dna Template

scholarly journals MethylExtract: High-Quality methylation maps and SNV calling from whole genome bisulfite sequencing data

F1000Research ◽  
2014 ◽  
Vol 2 ◽  
pp. 217 ◽  
Author(s):  
Guillermo Barturen ◽  
Antonio Rueda ◽  
José L. Oliver ◽  
Michael Hackenberg
Keyword(s):  
High Throughput ◽  
Sequence Variation ◽  
High Throughput Sequencing ◽  
Whole Genome ◽  
Single Nucleotide Variants ◽  
High Quality ◽  
Single Nucleotide ◽  
Error Sources ◽  
Link Type ◽  
Genome Methylation

Whole genome methylation profiling at a single cytosine resolution is now feasible due to the advent of high-throughput sequencing techniques together with bisulfite treatment of the DNA. To obtain the methylation value of each individual cytosine, the bisulfite-treated sequence reads are first aligned to a reference genome, and then the profiling of the methylation levels is done from the alignments. A huge effort has been made to quickly and correctly align the reads and many different algorithms and programs to do this have been created. However, the second step is just as crucial and non-trivial, but much less attention has been paid to the final inference of the methylation states. Important error sources do exist, such as sequencing errors, bisulfite failure, clonal reads, and single nucleotide variants.We developed MethylExtract, a user friendly tool to: i) generate high quality, whole genome methylation maps and ii) detect sequence variation within the same sample preparation. The program is implemented into a single script and takes into account all major error sources. MethylExtract detects variation (SNVs – Single Nucleotide Variants) in a similar way to VarScan, a very sensitive method extensively used in SNV and genotype calling based on non-bisulfite-treated reads. The usefulness of MethylExtract is shown by means of extensive benchmarking based on artificial bisulfite-treated reads and a comparison to a recently published method, called Bis-SNP.MethylExtract is able to detect SNVs within High-Throughput Sequencing experiments of bisulfite treated DNA at the same time as it generates high quality methylation maps. This simultaneous detection of DNA methylation and sequence variation is crucial for many downstream analyses, for example when deciphering the impact of SNVs on differential methylation. An exclusive feature of MethylExtract, in comparison with existing software, is the possibility to assess the bisulfite failure in a statistical way. The source code, tutorial and artificial bisulfite datasets are available at http://bioinfo2.ugr.es/MethylExtract/ and http://sourceforge.net/projects/methylextract/, and also permanently accessible from 10.5281/zenodo.7144.

scholarly journals All in One High Quality Genomic DNA and Total RNA Extraction From Nematode Induced Galls for High Throughput Sequencing Purposes

2019 ◽  
Vol 10 ◽  
Author(s):  
Ana Cláudia Silva ◽  
Virginia Ruiz-Ferrer ◽  
Ángela Martínez-Gómez ◽  
Marta Barcala ◽  
Carmen Fenoll ◽  
...  
Keyword(s):  
High Throughput ◽  
Genomic Dna ◽  
High Throughput Sequencing ◽  
Rna Extraction ◽  
High Quality ◽  
Total Rna ◽  
Total Rna Extraction

scholarly journals Pathology tissue-chromatin immunoprecipitation, coupled with high-throughput sequencing, allows the epigenetic profiling of patient samples

2010 ◽  
Vol 107 (50) ◽  
pp. 21535-21540 ◽  
Author(s):  
M. Fanelli ◽  
S. Amatori ◽  
I. Barozzi ◽  
M. Soncini ◽  
R. Dal Zuffo ◽  
...  
Keyword(s):  
High Throughput ◽  
Chromatin Immunoprecipitation ◽  
High Throughput Sequencing

scholarly journals Engineering the Compression of Sequencing Reads

2020 ◽  
Author(s):  
Tomasz Kowalski ◽  
Szymon Grabowski
Keyword(s):  
High Throughput ◽  
Compression Ratio ◽  
High Throughput Sequencing ◽  
Sequencing Data ◽  
Current Version ◽  
High Quality ◽  
High Throughput Sequencing Data ◽  
Compression Time ◽  
Practical Performance ◽  
Shortest Common Superstring

AbstractMotivationFASTQ remains among the widely used formats for high-throughput sequencing data. Despite advances in specialized FASTQ compressors, they are still imperfect in terms of practical performance tradeoffs.ResultsWe present a multi-threaded version of Pseudogenome-based Read Compressor (PgRC), an in-memory algorithm for compressing the DNA stream, based on the idea of building an approximation of the shortest common superstring over high-quality reads. The current version, v1.2, practically preserves the compression ratio and decompression speed of the previous one, reducing the compression time by a factor of about 4–5 on a 6-core/12-thread machine.AvailabilityPgRC 1.2 can be downloaded from https://github.com/kowallus/[email protected]

scholarly journals Overwintering honeybees maintained dynamic and stable intestinal bacteria

2021 ◽  
Author(s):  
Peng Liu ◽  
Yujie Zhu ◽  
Liang Ye ◽  
Tengfei Shi ◽  
Lai Li ◽  
...  
Keyword(s):  
16S Rdna ◽  
High Throughput ◽  
Beta Diversity ◽  
High Throughput Sequencing ◽  
Intestinal Bacteria ◽  
High Quality ◽  
Dynamic Changes ◽  
Ecological Balance ◽  
Significant Difference

Abstract Honeybee is an important pollinator for maintaining ecological balance. However, scientist found the bizarre mass death of bees in winter. Meanwhile, some reported that the differences composed of intestinal bacteria between healthy honeybees and CCD honeybees. It is essential that explored dynamic changes to the intestinal bacteria in overwintering honeybees. We collected bee samples before overwintering, during prophase of overwintering, metaphase of overwintering, anaphase of overwintering, telophase of overwintering, and after overwintering. By using high-throughput sequencing targeting the V3 − V4 regions of the 16S rDNA, the abundance of the intestinal bacteria were analyzed in overwintering honeybees. A total of 1,373,886 high-quality sequences were acquired and Proteobacteria (85.69%), Firmicutes (10.40%), Actinobacteria (3.66%), and Cyanobacteria (1.87%) were identified as major components of the intestinal bacteria. All core honeybee intestinal bacteria genera, such as Gilliamella, Bartonella, Snodgrassella, Lactobacillus, Frischella, Commensalibacter, and Bifidobacterium were detected. The abundance of Actinobacteria, Bartonella, and Bifidobacterium increased initially and then decreased in winter honeybees. There were no significant differences in the richness and evenness of the microbiota in overwintering honeybees; however, there was a statistically significant difference in the beta diversity of the intestinal bacteria after overwintering compared with that in other groups. Our results suggested that honeybees maintained their intestinal ecosystem balance, and increased the abundance of gut probiotics in response to environmental and nutrition pressures in winter.

Genome-wide mapping of endogenous G-quadruplex DNA structures by chromatin immunoprecipitation and high-throughput sequencing

2018 ◽  
Vol 13 (3) ◽  
pp. 551-564 ◽  
Author(s):  
Robert Hänsel-Hertsch ◽  
Jochen Spiegel ◽  
Giovanni Marsico ◽  
David Tannahill ◽  
Shankar Balasubramanian
Keyword(s):  
High Throughput ◽  
Chromatin Immunoprecipitation ◽  
High Throughput Sequencing ◽  
Quadruplex Dna ◽  
Dna Structures ◽  
Genome Wide ◽  
G Quadruplex

scholarly journals Perspectives and benefits of high-throughput long-read sequencing in microbial ecology

2021 ◽  
Author(s):  
Leho Tedersoo ◽  
Mads Albertsen ◽  
Sten Anslan ◽  
Benjamin Callahan
Keyword(s):  
Microbial Ecology ◽  
High Throughput ◽  
Single Molecule ◽  
High Throughput Sequencing ◽  
Environmental Dna ◽  
Nanopore Sequencing ◽  
High Quality ◽  
Short Read ◽  
Sequencing Technologies ◽  
Long Read

Short-read, high-throughput sequencing (HTS) methods have yielded numerous important insights into microbial ecology and function. Yet, in many instances short-read HTS techniques are suboptimal, for example by providing insufficient phylogenetic resolution or low integrity of assembled genomes. Single-molecule and synthetic long-read (SLR) HTS methods have successfully ameliorated these limitations. In addition, nanopore sequencing has generated a number of unique analysis opportunities such as rapid molecular diagnostics and direct RNA sequencing, and both PacBio and nanopore sequencing support detection of epigenetic modifications. Although initially suffering from relatively low sequence quality, recent advances have greatly improved the accuracy of long read sequencing technologies. In spite of great technological progress in recent years, the long-read HTS methods (PacBio and nanopore sequencing) are still relatively costly, require large amounts of high-quality starting material, and commonly need specific solutions in various analysis steps. Despite these challenges, long-read sequencing technologies offer high-quality, cutting-edge alternatives for testing hypotheses about microbiome structure and functioning as well as assembly of eukaryote genomes from complex environmental DNA samples.

Sign in / Sign up

Export Citation Format

Share Document