RNAflow: An Effective and Simple RNA-Seq Differential Gene Expression Pipeline Using Nextflow

Lataretu, Marie; Hölzer, Martin

doi:10.3390/genes11121487

Cited by 29 publications

(16 citation statements)

References 63 publications

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“…Degradation of RNA has been shown to impact this procedure and subsequent library preparation; [ 47 ] however, RNA quality numbers (RQN) of sequenced samples were within the recommended range (data not shown). Following other studies in which the same phenomenon was reported, including studies using IC‐BEVS, [ 23,48–50 ] reads mapped to rRNA were removed computationally to avoid its interference with differential expression analysis.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome analysis of Sf9 insect cells during production of recombinant Adeno‐associated virus

Virgolini

Hagan

Correia

et al. 2022

Biotechnology Journal

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The insect cell-baculovirus expression vector system (IC-BEVS) has emerged as an alternative time-and cost-efficient production platform for recombinant Adenoassociated virus (AAV) for gene therapy. However, a better understanding of the underlying biological mechanisms of IC-BEVS is fundamental to further optimize this expression system toward increased product titer and quality. Here, gene expression of Sf9 insect cells producing recombinant AAV through a dual baculovirus expression system, with low multiplicity of infection (MOI), was profiled by RNA-seq. An 8-fold increase in reads mapping to either baculovirus or AAV transgene sequences was observed between 24 and 48 h post-infection (hpi), confirming a take-over of the host cell transcriptome by the baculovirus. A total of 336 and 4784 genes were identified as differentially expressed at 24 hpi (vs non-infected cells) and at 48 hpi (vs. infected cells at 24 hpi), respectively, including dronc, birc5/iap5, and prp1. Functional annotation found biological processes such as cell cycle, cell growth, protein folding, and cellular amino acid metabolic processes enriched along infection. This work uncovers transcriptional changes in Sf9 in response to baculovirus infection, which provide new insights into cell and/or metabolic engineering targets that can be leveraged for rational bioprocess engineering of IC-BEVS for AAV production.

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Section: Discussionmentioning

confidence: 99%

Transcriptome analysis of Sf9 insect cells during production of recombinant Adeno‐associated virus

Virgolini

Hagan

Correia

et al. 2022

Biotechnology Journal

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“…The RNA ow differential gene expression pipeline v1.1.0 [24] was used for transcriptome analysis. This includes read quality control, count normalization, reference-based mapping, gene quanti cation, differential expression, and visualization.…”

Section: Methodsmentioning

confidence: 99%

Enhanced glycerol assimilation and lipid production in Rhodotorula toruloides CBS14 upon addition of hemicellulose primarily correlates with early transcription of energy-metabolism related genes

Martín-Hernández

Chmielarz

Müller

et al. 2022

Preprint

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Background Lipid formation from glycerol was previously found to be activated in Rhodotorula toruloides when the yeast was cultivated in a mixture of crude glycerol (CG) and hemicellulose hydrolysate (CGHH) compared to CG as the only carbon source. RNA samples from R. toruloides CBS14 cell cultures grown on either CG or CGHH were collected at different time points of cultivation, and a differential gene expression analysis was performed between cells grown at a similar physiological situation. Results We observed enhanced transcription of genes involved in oxidative phosphorylation and enzymes localized in mitochondria in CGHH compared to CG. Genes involved in protein turnover, including those encoding ribosomal proteins, translation elongation factors, and genes involved in building the proteasome also showed an enhanced transcription in CGHH compared to CG. At 10 h cultivation, another group of activated genes in CGHH was involved in β-oxidation, handling oxidative stress and degradation of xylose and aromatic compounds. Potential bypasses of the standard GUT1 and GUT2- glycerol assimilation pathway were also expressed and upregulated in CGHH 10 h. When the additional carbon sources from HH were completely consumed, at CGHH 36 h, their transcription decreased and NAD+-dependent glycerol-3-phosphate dehydrogenase was upregulated compared to CG 60 h, generating NADH instead of NADPH with glycerol catabolism. TPI1 was upregulated in CGHH compared to cells grown on CG in all physiological situations, potentially channeling the DHAP formed through glycerol catabolism into glycolysis. The highest number of upregulated genes encoding glycolytic enzymes was found after 36 h in CGHH, when all additional carbon sources were already consumed. Conclusions We suspect that the physiological reason for the activation of metabolism, which was the basis for the accelerated glycerol assimilation and faster lipid production, was primarily the activation of enzymes that provide energy.

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“…To quantify gene expression levels in the RNA-seq data, we used the nf-core/rnaseq pipeline. This pipeline is an open-source, community-driven pipeline for the analysis of RNA-seq data and is designed to be both reproducible and scalable (Lataretu and Hölzer, 2020). It includes a range of quality control checks, mapping of reads to a reference genome, and quantification of gene expression levels using count-based methods such as featureCounts.…”

Section: Rna-seq Read Mappingmentioning

confidence: 99%

Developing a non-invasive diagnostic model for pediatric Crohn’s disease using RNA-seq analysis

He¹,

Wang

Shu

et al. 2023

Front. Genet.

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Introduction: Pediatric Crohn’s disease is a chronic inflammatory condition that affects the digestive system in children and adolescents. It is characterized by symptoms such as abdominal pain, diarrhea, weight loss, and malnutrition, and can also cause complications like growth delays and delayed puberty. However, diagnosing pediatric Crohn’s disease can be difficult, especially when it comes to non-invasive methods.Methods: In this study, we developed a diagnostic model using RNA-seq to analyze gene expression in ileal biopsy samples from children with Crohn’s disease and non-pediatric Crohn’s controls.Results: Our results showed that pediatric Crohn’s disease is associated with altered expression of genes involved in immune response, inflammation, and tissue repair. We validated our findings using two independent datasets from the Gene Expression Omnibus (GEO) database, as well as through one prospective independent dataset, and found that our model had a high accuracy rate.Discussion: These findings suggest the possibility of non-invasive diagnosis for pediatric Crohn’s disease and may inform the development of targeted therapies for this condition.

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RNAflow: An Effective and Simple RNA-Seq Differential Gene Expression Pipeline Using Nextflow

Cited by 29 publications

References 63 publications

Transcriptome analysis of Sf9 insect cells during production of recombinant Adeno‐associated virus

Transcriptome analysis of Sf9 insect cells during production of recombinant Adeno‐associated virus

Enhanced glycerol assimilation and lipid production in Rhodotorula toruloides CBS14 upon addition of hemicellulose primarily correlates with early transcription of energy-metabolism related genes

Developing a non-invasive diagnostic model for pediatric Crohn’s disease using RNA-seq analysis

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