Computational Methods for Quality Check, Preprocessing and Normalization of RNA-Seq Data for Systems Biology and Analysis

Mazzoni, Gianluca; Kadarmideen, Haja N.

doi:10.1007/978-3-319-43332-5_3

Cited by 3 publications

(3 citation statements)

References 43 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The number of transcriptomic studies is rapidly growing, as researchers have targeted different tissues, experimental models, and biological conditions to identify differences in the abundance of the genes that underlie fertility-related traits. Similarly, several tools and methods have been proposed for transcriptomics analysis (reviewed in [78,79]). New opportunities have been unveiled by searching for circulating RNA molecules that could provide information on the physiological status of reproduction-related organs [80][81][82].…”

Section: Transcriptomicsmentioning

confidence: 99%

Harnessing Genomics and Transcriptomics Approaches to Improve Female Fertility in Beef Cattle—A Review

Kertz,

Banerjee,

Dyce

et al. 2023

Animals

View full text Add to dashboard Cite

Female fertility is the foundation of the cow–calf industry, impacting both efficiency and profitability. Reproductive failure is the primary reason why beef cows are sold in the U.S. and the cause of an estimated annual gross loss of USD 2.8 billion. In this review, we discuss the status of the genomics, transcriptomics, and systems genomics approaches currently applied to female fertility and the tools available to cow–calf producers to maximize genetic progress. We highlight the opportunities and limitations associated with using genomic and transcriptomic approaches to discover genes and regulatory mechanisms related to beef fertility. Considering the complex nature of fertility, significant advances in precision breeding will rely on holistic, multidisciplinary approaches to further advance our ability to understand, predict, and improve reproductive performance. While these technologies have advanced our knowledge, the next step is to translate research findings from bench to on-farm applications.

show abstract

Section: Transcriptomicsmentioning

confidence: 99%

Harnessing Genomics and Transcriptomics Approaches to Improve Female Fertility in Beef Cattle—A Review

Kertz,

Banerjee,

Dyce

et al. 2023

Animals

View full text Add to dashboard Cite

show abstract

“…For a more detailed description of the general RNA-seq workflow there are a number of informative reviews covering this topic in a non-taxon-specific manner (Bullard et al 2010;Conesa et al 2016;Mazzoni and Kadarmideen 2016;Oshlack et al 2010;Vijay et al 2013;Wang et al 2009;Wolf 2013). In the "Planning an RNA-seq study: a quick guide" section of this review, we will further give a quick guide on what to take into consideration when planning an RNA-seq study in birds.…”

Section: Microarray Analysismentioning

confidence: 99%

“…We will further point the reader to more detailed literature for each step of the workflow. There are currently a number of reviews, tutorials and best practise guides available that should be used in parallel to find more in depth information on how to plan and smoothly undertake transcriptomics studies (Bullard et al 2010;Conesa et al 2016;Mazzoni and Kadarmideen 2016;Oshlack et al 2010;Teng et al 2016;Vijay et al 2013;Wang et al 2009;Wolf 2013). Eventually, early meetings with one's local sequencing core facility and/ or a commercial provider should be sought for details.…”

Section: Planning An Rna-seq Study: a Quick Guidementioning

confidence: 99%

Avian transcriptomics: opportunities and challenges

Jax

Kraus

2018

J Ornithol

View full text Add to dashboard Cite

Recent developments in next-generation sequencing technologies have greatly facilitated the study of whole transcriptomes in model and non-model species. Studying the transcriptome and how it changes across a variety of biological conditions has had major implications for our understanding of how the genome is regulated in different contexts, and how to interpret adaptations and the phenotype of an organism. The aim of this review is to highlight the potential of these new technologies for the study of avian transcriptomics, and to summarise how transcriptomics has been applied in ornithology. A total of 81 peer-reviewed scientific articles that used transcriptomics to answer questions within a broad range of study areas in birds are used as examples throughout the review. We further provide a quick guide to highlight the most important points which need to be take into account when planning a transcriptomic study in birds, and discuss how researchers with little background in molecular biology can avoid potential pitfalls. Suggestions for further reading are supplied throughout. We also discuss possible future developments in the technology platforms used for ribonucleic acid sequencing. By summarising how these novel technologies can be used to answer questions that have long been asked by ornithologists, we hope to bridge the gap between traditional ornithology and genomics, and to stimulate more interdisciplinary research.

show abstract

Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

et al. 2018

View full text Add to dashboard Cite

BackgroundMammalian phenotypes are shaped by numerous genome variants, many of which may regulate gene transcription or RNA splicing. To identify variants with regulatory functions in cattle, an important economic and model species, we used sequence variants to map a type of expression quantitative trait loci (expression QTLs) that are associated with variations in the RNA splicing, i.e., sQTLs. To further the understanding of regulatory variants, sQTLs were compare with other two types of expression QTLs, 1) variants associated with variations in gene expression, i.e., geQTLs and 2) variants associated with variations in exon expression, i.e., eeQTLs, in different tissues.ResultsUsing whole genome and RNA sequence data from four tissues of over 200 cattle, sQTLs identified using exon inclusion ratios were verified by matching their effects on adjacent intron excision ratios. sQTLs contained the highest percentage of variants that are within the intronic region of genes and contained the lowest percentage of variants that are within intergenic regions, compared to eeQTLs and geQTLs. Many geQTLs and sQTLs are also detected as eeQTLs. Many expression QTLs, including sQTLs, were significant in all four tissues and had a similar effect in each tissue. To verify such expression QTL sharing between tissues, variants surrounding (±1 Mb) the exon or gene were used to build local genomic relationship matrices (LGRM) and estimated genetic correlations between tissues. For many exons, the splicing and expression level was determined by the same cis additive genetic variance in different tissues. Thus, an effective but simple-to-implement meta-analysis combining information from three tissues is introduced to increase power to detect and validate sQTLs. sQTLs and eeQTLs together were more enriched for variants associated with cattle complex traits, compared to geQTLs. Several putative causal mutations were identified, including an sQTL at Chr6:87392580 within the 5th exon of kappa casein (CSN3) associated with milk production traits.ConclusionsUsing novel analytical approaches, we report the first identification of numerous bovine sQTLs which are extensively shared between multiple tissue types. The significant overlaps between bovine sQTLs and complex traits QTL highlight the contribution of regulatory mutations to phenotypic variations.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4902-8) contains supplementary material, which is available to authorized users.

show abstract

Computational Methods for Quality Check, Preprocessing and Normalization of RNA-Seq Data for Systems Biology and Analysis

Cited by 3 publications

References 43 publications

Harnessing Genomics and Transcriptomics Approaches to Improve Female Fertility in Beef Cattle—A Review

Harnessing Genomics and Transcriptomics Approaches to Improve Female Fertility in Beef Cattle—A Review

Avian transcriptomics: opportunities and challenges

Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Contact Info

Product

Resources

About