Synthetic data sets for the identification of key ingredients for RNA-seq differential analysis

Rigaill, Guillem; Balzergue, Sandrine; Brunaud, Véronique; Blondet, Eddy; Rau, Andrea; Rogier, Odile; Caïus, José; Maugis-Rabusseau, Cathy; Soubigou‐Taconnat, Ludivine; Aubourg, Santiago P.; Lurin, Claire; Martin‐Magniette, Marie‐Laure; Delannoy, Étienne

doi:10.1093/bib/bbw092

Cited by 48 publications

(54 citation statements)

References 39 publications

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“…Here we summarize considerations for avian epigenome investigation from sequencing considerations to the data analysis involving huge datasets. The importance of a carefully designed and executed experimental design has been addressed in previous reports [90,91]. In particular, experimental design should take into account parental history (such as rearing conditions and nutrition) and hatchery practices.…”

Section: Design Of Epigenomic Studiesmentioning

confidence: 99%

Genome-Wide Epigenetic Studies in Chicken: A Review

David¹,

Mersch

Foissac

et al. 2017

Epigenomes

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Over the years, farmed birds have been selected on various performance traits mainly through genetic selection. However, many studies have shown that genetics may not be the sole contributor to phenotypic plasticity. Gene expression programs can be influenced by environmentally induced epigenetic changes that may alter the phenotypes of the developing animals. Recently, high-throughput sequencing techniques became sufficiently affordable thanks to technological advances to study whole epigenetic landscapes in model plants and animals. In birds, a growing number of studies recently took advantage of these techniques to gain insights into the epigenetic mechanisms of gene regulation in processes such as immunity or environmental adaptation. Here, we review the current gain of knowledge on the chicken epigenome made possible by recent advances in high-throughput sequencing techniques by focusing on the two most studied epigenetic modifications, DNA methylation and histone post-translational modifications. We discuss and provide insights about designing and performing analyses to further explore avian epigenomes. A better understanding of the molecular mechanisms underlying the epigenetic regulation of gene expression in relation to bird phenotypes may provide new knowledge and markers that should undoubtedly contribute to a sustainable poultry production.

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Section: Design Of Epigenomic Studiesmentioning

confidence: 99%

Genome-Wide Epigenetic Studies in Chicken: A Review

David¹,

Mersch

Foissac

et al. 2017

Epigenomes

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“…The distribution of the resulting p‐values followed the quality criterion described by Rigaill et al . (). The Benjamini−Hochberg correction was used to control false discovery rate (FDR; Benjamini and Hochberg, ).…”

Section: Methodsmentioning

confidence: 97%

“…In our model, the log2ratio was expressed as a linear combination of a species effect and the p-values corresponding to the contrasts described in Data S1 were calculated. The distribution of the resulting p-values followed the quality criterion described by Rigaill et al (2018). The BenjaminiÀHochberg correction was used to control false discovery rate (FDR; Benjamini and Hochberg, 1995).…”

Section: Statisticsmentioning

confidence: 99%

In situ transcriptomic and metabolomic study of the loss of photosynthesis in the leaves of mixotrophic plants exploiting fungi

et al. 2019

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Summary Mycoheterotrophic plants have lost photosynthesis and obtain carbon through mycorrhizal fungi colonizing their roots. They are likely to have evolved from mixotrophic ancestors, which rely on both photosynthesis and fungal carbon for their development. Whereas our understanding of the ecological and genomic changes associated with the evolutionary shift to mycoheterotrophy is deepening, little information is known about the specific metabolic and physiological features driving this evolution. We investigated this issue in naturally occurring achlorophyllous variants of temperate mixotrophic orchids. We carried out an integrated transcriptomic and metabolomic analysis of the response to achlorophylly in the leaves of three mixotrophic species sampled in natura. Achlorophyllous leaves showed major impairment of their photosynthetic and mineral nutrition functions, strong accumulation of free amino acids, overexpression of enzymes and transporters related to sugars, amino acids and fatty acid catabolism, as well as induction of some autophagy‐related and biotic stress genes. Such changes were reminiscent of these reported for variegated leaves and appeared to be symptomatic of a carbon starvation response. Rather than decisive metabolic innovations, we suggest that the evolution towards mycoheterotrophy in orchids is more likely to be reliant on the versatility of plant metabolism and an ability to exploit fungal organic resources, especially amino acids, to replace missing photosynthates.

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“…Choices for the differential analysis were made based on Rigaill et al, 2018. To increase the detection power by limiting the number of statistical tests (Bourgon et al, 2010) we performed an independent filtering by discarding genes which did not have at least 1 read after a count per million analysis (CPM) in at least one half of the samples.…”

Section: Rna-seq Read Processing and Gene Expression Analysismentioning

confidence: 99%

Transcriptomics at maize embryo/endosperm interfaces identify a novel transcriptionally distinct endosperm sub-domain adjacent to the embryo scutellum (EAS)

Doll

Just

Brunaud

et al. 2019

Preprint

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Seeds are complex biological systems comprising three genetically distinct tissues nested one inside another (embryo, endosperm and maternal tissues). However, the complexity of the kernel makes it difficult to understand inter compartment interactions without access to spatially accurate information. Here we took advantage of the large size of the maize kernel to characterize genome-wide expression profiles of tissues at embryo/endosperm interfaces.Our analysis identifies specific transcriptomic signatures in two interface tissues compared to whole seed compartments: The scutellar aleurone layer (SAL), and the newly named endosperm adjacent to scutellum (EAS). The EAS, which appears around 9 days after pollination and persists for around 11 days, is confined to one to three endosperm cell layers adjacent to the embryonic scutellum. Its transcriptome is enriched in genes encoding transporters. The absence of the embryo in an embryo specific (emb) mutant can alter the expression pattern of EAS marker genes. The detection of cell death in some EAS cells together with an accumulation of crushed cell walls suggests that the EAS is a dynamic zone from which cell layers in contact with the embryo are regularly eliminated, and to which additional endosperm cells are recruited as the embryo grows.

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Synthetic data sets for the identification of key ingredients for RNA-seq differential analysis

Cited by 48 publications

References 39 publications

Genome-Wide Epigenetic Studies in Chicken: A Review

Genome-Wide Epigenetic Studies in Chicken: A Review

In situ transcriptomic and metabolomic study of the loss of photosynthesis in the leaves of mixotrophic plants exploiting fungi

Transcriptomics at maize embryo/endosperm interfaces identify a novel transcriptionally distinct endosperm sub-domain adjacent to the embryo scutellum (EAS)

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