smallrnaseq: short non coding RNA-Seq analysis with Python

Farrell, DJ

doi:10.1101/110585

Cited by 5 publications

(4 citation statements)

References 33 publications

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“…Files containing microRNA counts and gene counts are located in the GEO database. Small RNA samples were processed using the smallrnaseq python tool ( 20 ), which aligns samples using Bowtie and quantifies small RNA read counts using reference fasta and gtf files from RNAcentral.org .…”

Section: Methodsmentioning

confidence: 99%

RNA Sequencing Reveals Key Metabolic Pathways Are Modified by Short-Term Whole Egg Consumption

et al. 2021

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Eggs are protein-rich, nutrient-dense, and contain bioactive ingredients that have been shown to modify gene expression and impact health. To understand the effects of egg consumption on tissue-specific mRNA and microRNA expression, we examined the role of whole egg consumption (20% protein, w/w) on differentially expressed genes (DEGs) between rat (n = 12) transcriptomes in the prefrontal cortex (PFC), liver, kidney, and visceral adipose tissue (VAT). Principal component analysis with hierarchical clustering was used to examine transcriptome profiles between dietary treatment groups. We performed Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis as well as genetic network and disease enrichment analysis to examine which metabolic pathways were the most predominantly altered in each tissue. Overall, our data demonstrates that whole egg consumption for 2 weeks modified the expression of 52 genes in the PFC, 22 genes in VAT, and two genes in the liver (adj p < 0.05). Additionally, 16 miRNAs were found to be differentially regulated in the PFC, VAT, and liver, but none survived multiple testing correction. The main pathways influenced by WE consumption were glutathione metabolism in VAT and cholesterol biosynthesis in the PFC. These data highlight key pathways that may be involved in diseases and are impacted by acute consumption of a diet containing whole eggs.

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Section: Methodsmentioning

confidence: 99%

RNA Sequencing Reveals Key Metabolic Pathways Are Modified by Short-Term Whole Egg Consumption

et al. 2021

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“…For smallRNA samples, reference fasta files from www.RNACentral.org were downloaded for microRNA, piwiRNA, snRNA, nRNA, rRNA, and tRNA. Indexes were generated using Bowtie [ 50 ] and alignment was conducted using the smallrnaseq python tool [ 51 ]. Read counts for all reference indices and IsomiRs were generated using the smallrnaseq python tool.…”

Section: Methodsmentioning

confidence: 99%

“…All microRNA fastq files were processed using the smallrnaseq [ 51 ] package in python. Smallrnaseq automates standard bioinformatic processes for quantification and analysis of small non-coding RNA species such as microRNA quantification and novel microRNA prediction.…”

Section: Methodsmentioning

confidence: 99%

Whole egg consumption increases gene expression within the glutathione pathway in the liver of Zucker Diabetic Fatty rats

et al. 2020

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Nutrigenomic evidence supports the idea that Type 2 Diabetes Mellitus (T2DM) arises due to the interactions between the transcriptome, individual genetic profiles, lifestyle, and diet. Since eggs are a nutrient dense food containing bioactive ingredients that modify gene expression, our goal was to examine the role of whole egg consumption on the transcriptome during T2DM. We analyzed whether whole egg consumption in Zucker Diabetic Fatty (ZDF) rats alters microRNA and mRNA expression across the adipose, liver, kidney, and prefrontal cortex tissue. Male ZDF (fa/fa) rats ( n = 12) and their lean controls (fa/+) ( n = 12) were obtained at 6 wk of age. Rats had ad libitum access to water and were randomly assigned to a modified semi-purified AIN93G casein-based diet or a whole egg-based diet, both providing 20% protein (w/w). TotalRNA libraries were prepared using QuantSeq 3' mRNA-Seq and Lexogen smallRNA library prep kits and were further sequenced on an Illumina HighSeq3000. Differential gene expression was conducted using DESeq2 in R and Benjamini-Hochberg adjusted P -values controlling for false discovery rate at 5%. We identified 9 microRNAs and 583 genes that were differentially expressed in response to 8 wk of consuming whole egg-based diets. Kyto Encyclopedia of Genes and Genomes/Gene ontology pathway analyses demonstrated that 12 genes in the glutathione metabolism pathway were upregulated in the liver and kidney of ZDF rats fed whole egg. Whole egg consumption primarily altered glutathione pathways such as conjugation, methylation, glucuronidation, and detoxification of reactive oxygen species. These pathways are often negatively affected during T2DM, therefore this data provides unique insight into the nutrigenomic response of dietary whole egg consumption during the progression of T2DM.

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“…Vitamin D3 can be primarily found in two forms in food, the biologically active steroid hormone 1-25-OH-vitD3 (1,25D3) and the main circulating form 25-OH-vitD3 (25D3) [135]. A single large egg can contain between 50 to 500 IU of 1-25D3 and 25D3 [46], which directly affects the transcriptome by modifying gene expression across the entire human genome through interactions with the vitamin D receptor [47]. Vitamin D is known to regulate calcium homeostasis, immune function and suboptimal vitamin D levels may contribute to the onset or progression of osteoporosis, sarcopenia, depression [48], neurodegenerative diseases [49], and even specific forms of cancer [50].…”

Section: Composition Of Whole Eggs and Bioactive Mechanisms Of Actionmentioning

confidence: 99%

Nutrigenomics and aging: A transcriptomic perspective

Webb¹

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Nutrients Vitamins Minerals MOISTURE-g (75.81) NIACIN-mg (0.103) CALCIUM-mg (55) FAT-g (total lipid) (10.3) RIBOFLAVIN-mg (0.523) IRON-mg (1.77) ASH-g (1.16) B12-mcg (1) MAGNESIUM-mg (11.2) CARBOHYDRATE-g (0.91) PANTOTHENIC ACID-mg (1.57) PHOSPHORUS-mg (189) GLUCOSE-g (0.25) VITAMIN A-IU (570) POTASSIUM-mg (117) CALORIES-kcal (150) THIAMIN-mg (0.067) SODIUM-mg (121) CHOLESTEROL-mg (420) PYRIDOXINE (B6)-mg (0.188) ZINC-mg (1.2)

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smallrnaseq: short non coding RNA-Seq analysis with Python

Cited by 5 publications

References 33 publications

RNA Sequencing Reveals Key Metabolic Pathways Are Modified by Short-Term Whole Egg Consumption

RNA Sequencing Reveals Key Metabolic Pathways Are Modified by Short-Term Whole Egg Consumption

Whole egg consumption increases gene expression within the glutathione pathway in the liver of Zucker Diabetic Fatty rats

Nutrigenomics and aging: A transcriptomic perspective

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