PoplarV1, Main, Exploration, bibRecord, 002242

Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees.

Identifieur interne : 002242 ( Main/Exploration ); précédent : 002241; suivant : 002243

Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees.

Auteurs : Lijun Liu ; Victor Missirian ; Matthew Zinkgraf ; Andrew Groover ; Vladimir Filkov

Source :

BMC genomics [ 1471-2164 ] ; 2014.

RBID : pubmed:25081589

Descripteurs français

English descriptors

KwdEn :
- Chromatin Immunoprecipitation (MeSH), Chromosome Mapping (MeSH), Computational Biology (MeSH), Gene Library (MeSH), High-Throughput Nucleotide Sequencing (MeSH), Populus (genetics), RNA Polymerase II (genetics), RNA, Plant (genetics), Research Design (MeSH), Sequence Analysis, RNA (MeSH), Transcription Factors (genetics).
MESH :
- chemical , genetics : RNA Polymerase II, RNA, Plant, Transcription Factors.
- genetics : Populus.
- Chromatin Immunoprecipitation, Chromosome Mapping, Computational Biology, Gene Library, High-Throughput Nucleotide Sequencing, Research Design, Sequence Analysis, RNA.

Abstract

BACKGROUND

One of the great advantages of next generation sequencing is the ability to generate large genomic datasets for virtually all species, including non-model organisms. It should be possible, in turn, to apply advanced computational approaches to these datasets to develop models of biological processes. In a practical sense, working with non-model organisms presents unique challenges. In this paper we discuss some of these challenges for ChIP-seq and RNA-seq experiments using the undomesticated tree species of the genus Populus.

RESULTS

We describe specific challenges associated with experimental design in Populus, including selection of optimal genotypes for different technical approaches and development of antibodies against Populus transcription factors. Execution of the experimental design included the generation and analysis of Chromatin immunoprecipitation-sequencing (ChIP-seq) data for RNA polymerase II and transcription factors involved in wood formation. We discuss criteria for analyzing the resulting datasets, determination of appropriate control sequencing libraries, evaluation of sequencing coverage needs, and optimization of parameters. We also describe the evaluation of ChIP-seq data from Populus, and discuss the comparison between ChIP-seq and RNA-seq data and biological interpretations of these comparisons.

CONCLUSIONS

These and other "lessons learned" highlight the challenges but also the potential insights to be gained from extending next generation sequencing-supported network analyses to undomesticated non-model species.

DOI: 10.1186/1471-2164-15-S5-S3
PubMed: 25081589
PubMed Central: PMC4120141

Affiliations:

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Le document en format XML

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<author><name sortKey="Zinkgraf, Matthew" sort="Zinkgraf, Matthew" uniqKey="Zinkgraf M" first="Matthew" last="Zinkgraf">Matthew Zinkgraf</name>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Chromatin Immunoprecipitation (MeSH)</term>
<term>Chromosome Mapping (MeSH)</term>
<term>Computational Biology (MeSH)</term>
<term>Gene Library (MeSH)</term>
<term>High-Throughput Nucleotide Sequencing (MeSH)</term>
<term>Populus (genetics)</term>
<term>RNA Polymerase II (genetics)</term>
<term>RNA, Plant (genetics)</term>
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<term>Banque de gènes (MeSH)</term>
<term>Biologie informatique (MeSH)</term>
<term>Cartographie chromosomique (MeSH)</term>
<term>Facteurs de transcription (génétique)</term>
<term>Immunoprécipitation de la chromatine (MeSH)</term>
<term>Plan de recherche (MeSH)</term>
<term>Populus (génétique)</term>
<term>RNA polymerase II (génétique)</term>
<term>Séquençage nucléotidique à haut débit (MeSH)</term>
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<keywords scheme="MESH" xml:lang="en"><term>Chromatin Immunoprecipitation</term>
<term>Chromosome Mapping</term>
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<term>Gene Library</term>
<term>High-Throughput Nucleotide Sequencing</term>
<term>Research Design</term>
<term>Sequence Analysis, RNA</term>
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<front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b>
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<p>One of the great advantages of next generation sequencing is the ability to generate large genomic datasets for virtually all species, including non-model organisms. It should be possible, in turn, to apply advanced computational approaches to these datasets to develop models of biological processes. In a practical sense, working with non-model organisms presents unique challenges. In this paper we discuss some of these challenges for ChIP-seq and RNA-seq experiments using the undomesticated tree species of the genus Populus.</p>
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<div type="abstract" xml:lang="en"><p><b>RESULTS</b>
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<p>We describe specific challenges associated with experimental design in Populus, including selection of optimal genotypes for different technical approaches and development of antibodies against Populus transcription factors. Execution of the experimental design included the generation and analysis of Chromatin immunoprecipitation-sequencing (ChIP-seq) data for RNA polymerase II and transcription factors involved in wood formation. We discuss criteria for analyzing the resulting datasets, determination of appropriate control sequencing libraries, evaluation of sequencing coverage needs, and optimization of parameters. We also describe the evaluation of ChIP-seq data from Populus, and discuss the comparison between ChIP-seq and RNA-seq data and biological interpretations of these comparisons.</p>
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<div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b>
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<p>These and other "lessons learned" highlight the challenges but also the potential insights to be gained from extending next generation sequencing-supported network analyses to undomesticated non-model species.</p>
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Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees.

Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees.

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Abstract

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