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opencc-zeroJan 2022View details →

Gene expression profiles compared in environmental and malnutrition enteropathy in Zambian children and adults

Background: Environmental enteropathy (EE) contributes to growth failure in millions of children worldwide, but its relationship to clinical malnutrition has not been elucidated. We used RNA sequencing to compare duodenal biopsies from adults and children with EE, and from children with severe acute malnutrition (SAM), to define key features of these malnutrition-related enteropathies. Methods: RNA was extracted and sequenced from biopsies of children with SAM in hospital (n=27), children with non-responsive stunting in the community (n=30), and adults living in the same community (n=37) using an identical sequencing and analysis pipeline. Two biopsies each were profiled and differentially expressed genes (DEGs) were computed from the comparisons of the three groups. DEG lists from these comparisons were then subjected to analysis with CompBio software to assemble a holistic view of the biological landscape and IPA software to interrogate canonical pathways. Findings: Dysregulation was identified in goblet cell/mucin production and xenobiotic metabolism/detoxification for both cohorts of children, versus adults. Within the SAM cohort, substantially greater induction of immune response and barrier function, including NADPH oxidases was noted, concordant with broadly reduced expression of genes associated with the brush border and intestinal structure/transport/absorption. Interestingly, down regulation of genes associated with the hypothalamic-pituitary-adrenal axis was selectively observed within the cohort of children with stunting. Interpretation: Gene expression profiles in environmental enteropathy and severe acute malnutrition have similarities, but SAM has several distinct transcriptional features. The intestinal capacity to metabolise drugs and toxins in malnourished children requires further study.

opencc-by-4.0Oct 2017View details →

ROS-specific Huntingtin Interactions: Comparing transfection methods for inducible expression of huntingtin-specific chromobody

Optimization step in the development of an inducible system expressing YFP-tagged huntingtin-specific intrabodies for stable transfection in TruHD fibroblasts.

opencc-by-4.0Aug 2024View details →

Life in the fastlane? A comparative analysis of gene expression profiles across annual, semi-annual, and non-annual killifishes (Cyprinodontiformes: Nothobranchiidae)

<ol> <li>Read Counts per gene</li> <li>All read counts by inidividual and species</li> <li>Species abbreviations key</li> <li>R script for data analyses</li> </ol>

opencc-by-4.0Feb 2024View details →

Assessment of changes in circRNA expression based on transcripts of genes encoding ADAMTS proteins in patients with non-small cell lung carcinoma compared to normal tissue

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opencc-zeroJan 2020View details →

RNA-seq reveals altered gene expression levels in proximal tubular cell cultures compared to renal cortex but not during early glucotoxicity

AbstractCell cultures are often used to study physiological processes in health and disease. It is well-known that cells change their gene expression in vitro compared to in vivo, but it is rarely experimentally addressed. High glucose is a known trigger of apoptosis in proximal tubular cells (PTC). Here we used RNA-seq to detect differentially expressed genes in cultures of primary rat PTC, 3 days old, compared to cells retrieved directly from rat outer renal cortex and between PTC exposed to 15 mM glucose and control for 8 h. The expression of 6,174 genes was significantly up- or downregulated in the cultures of PTC compared to the cells in the outer renal cortex. Most altered were mitochondrial and metabolism related genes. Gene expression of proapoptotic proteins were upregulated and gene expression of antiapoptotic proteins were downregulated in PTC. Expression of transporter related genes were generally downregulated. After 8 h, high glucose had not altered the gene expression in PTC. The current study provides evidence that cells alter their gene expression in vitro compared to in vivo and suggests that short-term high glucose exposure can trigger apoptosis in PTC without changing the gene expression levels of apoptotic proteins.

opencc-zeroSep 2023View details →

Data from: A comparative analysis of stably expressed genes across diverse angiosperms exposes flexibility in underlying promoter architecture

Promoters regulate both the amplitude and pattern of gene expression—key factors needed for optimization of many synthetic biology applications. Previous work in Arabidopsis found that promoters that contain a TATA-box element tend to be expressed only under specific conditions or in particular tissues, while promoters which lack any known promoter elements, thus designated as Coreless, tend to be expressed more ubiquitously. To test whether this trend represents a conserved promoter design rule, we identified stably expressed genes across multiple angiosperm species using publicly available RNA-seq data. Comparisons between core promoter architectures and gene expression stability revealed differences in core promoter usage in monocots and eudicots. Furthermore, when tracing the evolution of a given promoter across species, we found that core promoter type was not a strong predictor of expression stability. Our analysis suggests that core promoter types are correlative rather than causative in promoter expression patterns and highlights the challenges in finding or building constitutive promoters that will work across diverse plant species.

opencc-by-4.0Sep 2023View details →

Comparative Analysis of Maternal Gene Expression Patterns: Unraveling Evolutionary Signatures Across Reproductive Modes

Dataset used to reproduce the analysis performed in "Comparative Analysis of Maternal Gene Expression Patterns: Unraveling Evolutionary Signatures Across Reproductive Modes" publication. The directory structure is the following: <ul> <li>Gene_models - directory containing gene models (.gtf or .gff3 files) used for feature length comparisons across species</li> <li>intermediate_data - directory containing intermediate results from various scripts, the main purpose is to speed up the reproducibility of some longer running scripts <ul> <li>batch_adjusted_normalised_gene_expression_matrix.tsv - gene expression matrix used for evolutionary model fitting</li> <li>fc.tsv - fold change matrix used for evolutionary model fitting</li> <li>dated_species_tree.tre - species tree used throughout the model fitting step (newick format)</li> <li>DGE_script_enviorment.RData - saved R environment from differential gene expression analysis</li> <li>downregulated_IDs.RDS - gene IDs which undergo down-regulation throughout maternal-to-zygotic transition</li> <li>maternal_IDs.RDS - gene IDs which meet the cut-off criteria for being considered as maternally expressed</li> <li>N0_blasted.tsv - orthogroup annotations through blasting to a sequence database</li> <li>N0.tsv - orthogroups inferred from OrthoFinder</li> <li>OG_categories.tsv - classification of orthogroups based on them (I) having genes with maternal expression, but no significant down regulation, (II) having genes with maternal expression and significant down regulation throughout maternal-to-zygotic transition or (III) no maternal expression</li> <li>OG_presence.tsv - binary matrix coding for which orthogroup which species have gene expression values</li> <li>Paralog_variances.tsv - matrix containing variance metrics for paralogs in each species from before normalization across species</li> </ul> </li> <li>Pannzer2_annotation - directory containing GO annotations for all species from the Pannzer2 tool, used for GO analyses</li> <li>quantification_files - directory containing all salmon quantification outputs</li> <li>transcriptomes - de novo assembled transcriptomes for non-model species</li> </ul>

publicSep 2023View details →

Data from: A comparative analysis of stably expressed genes across diverse angiosperms exposes flexibility in underlying promoter architecture

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publicAug 2025View details →

Data from: Comparative analysis of convergent jellyfish eyes reveals extensive differences in expression of vision-related genes

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publicJan 2022View details →

Gene expression profiles compared in environmental and malnutrition enteropathy in Zambian children and adults

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publicJan 2020View details →

RNA-seq reveals altered gene expression levels in proximal tubular cell cultures compared to renal cortex but not during early glucotoxicity

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opencc-zeroDec 2019View details →

Comparative gene expression analysis reveals mechanism of Pinus contorta response to the fungal pathogen Dothistroma septosporum

Many conifers have distributions that span wide ranges in both biotic and abiotic conditions, but the basis of response to biotic stress has received much less attention than response to abiotic stress. In this study, we investigated the gene expression response of lodgepole pine (Pinus contorta) to attack by the fungal pathogen Dothistroma septosporum, which causes Dothistroma needle blight (DNB), a disease that has caused severe climate-related outbreaks in northwestern British Columbia. We inoculated tolerant and susceptible pines with two D. septosporum isolates and analyzed the differentially expressed genes, differential exon usage, and co-expressed gene modules using RNA-seq data. We found a rapid and strong transcriptomic response in tolerant lodgepole pine samples inoculated with one D. septosporum isolate, and a late and weak response in susceptible samples inoculated with another isolate. We mapped 43 of the DEG- or gene-module-identified genes to the reference plant-pathogen interaction pathway deposited in KEGG database. These genes are present in PAMP-triggered and effector-triggered immunity pathways, including genes encoding mitogen-activated protein kinase and disease resistance protein. Genes comprising pathways and gene modules had signatures of strong selective constraint, while the highly expressed genes in tolerant samples appear to have been favored by selection to counterattack the pathogen. We identified candidate resistance genes that may respond to D. septosporum effectors. Taken together, our results show that gene expression response to D. septosporum infection in lodgepole pine varies both among tree genotypes and pathogen strains, and involves both known candidate genes and a number of genes with previously unknown functions.

opencc-zeroDec 2016View details →

Data from: Comparative ecological transcriptomics and the contribution of gene expression to the evolutionary potential of a threatened fish

Understanding whether small populations with low genetic diversity can respond to rapid environmental change via phenotypic plasticity is an outstanding research question in biology. RNA sequencing (RNA-seq) has recently provided the opportunity to examine variation in gene expression, a surrogate for phenotypic variation, in non-model species. We used a comparative RNA-seq approach to assess expression variation within and among adaptively divergent populations of a threatened freshwater fish, Nannoperca australis, found across a steep hydroclimatic gradient in the Murray-Darling Basin, Australia. These populations evolved under contrasting selective environments (e.g. dry/hot lowland; wet/cold upland) and represent opposite ends of the species' spectrum of genetic diversity and population size. We tested the hypothesis that environmental variation among isolated populations has driven the evolution of divergent expression at ecologically important genes using differential expression (DE) analysis and an ANOVA-based comparative phylogenetic expression variance and evolution model framework based on 27,425 de novo assembled transcripts. Additionally, we tested whether gene expression variance within-populations was correlated with levels of standing genetic diversity. We identified 290 DE candidate transcripts, 33 transcripts with evidence for high expression plasticity, and 50 candidates for divergent selection on gene expression after accounting for phylogenetic structure. Variance in gene expression appeared unrelated to levels of genetic diversity. Functional annotation of the candidate transcripts revealed variation in water quality is an important factor influencing expression variation for N. australis. Our findings suggest that gene expression variation can contribute to the evolutionary potential of small populations.

zenodo32/100

Comparative analysis of statistical methods used for detecting differential expression in label-free mass spectrometry proteomics - Data Supplement

This the is Data Supplement for the article "Comparative analysis of statistical methods used for detecting differential expression in label-free mass spectrometry proteomics" submitted to the Journal of Proteomics 2015.

opencc-zeroJun 2015View details →

opencc-zeroNov 2021View details →

Data from: The transcriptomics of crushing jaw convergence in cichlid fishes: comparative gene expression in recent sympatric versus older allopatric trophic adaptations

How gene expression diverges during adaptation might be strongly influenced by the geographic setting and timeframe over which species evolve. To contrast transcriptomic patterns of replicate trophic adaptations that evolved convergently during both allopatric and sympatric contexts, we conducted RNA-seq on the trophically important lower pharyngeal jaws of two sympatrically and four allopatrically diverged species pairs of cichlid fishes. We first show that all of these species pairs have convergently diverged along a crushing trophic axis and that the sympatric pairs are as phenotypically divergent as the allopatric pairs. Then, we found that distinct sets of genes were differentially expressed in the jaws of sympatrically diverging pairs as compared to jaws in older allopatric species pairs. The genes that were differentially expressed in the jaws of allopatric pairs also were more highly expressed on average than in the sympatric pairs. Finally, for genes that were differentially expressed, the magnitude of differences in expression between the jaws were greater for sympatrically diverging species pairs. The particular genes, their expression levels, and the magnitude of expression differences between sympatrically originating adaptations might all play an important role in generating and maintaining boundaries to gene flow during the rapid ecological divergence that often characterizes sympatric speciation.

zenodo32/100

Comparative analysis of differential gene expression indicates divergence in ontogenetic strategies of leaves in two conifer genera

Juniperus flaccida (drooping juniper) and Pinus cembroides (pinyon pine) are conifers native to North America, spanning Mexico and the Southwestern region of the United States. Although from two different lineages, both species exhibit heteroblastic growth. Morphologically, their leaves undergo a change between the juvenile and adult life stage. J. flaccida leaves appear needle-like at youth and scale-like at maturity, whereas the P. cembroides will transition from needle-like leaves to brown scale-like leaves. The objective was to perform a comparative transcriptomic analysis to quantify and examine differential expression in juvenile and adult individuals from both species. RNA from twelve samples was sequenced on HiSeq 1500 (100bp PE) and analyzed with available software. Because there are no reference genomes for these species, they were assembled de novo from the RNA-Seq reads. Following assembly, the coding regions were identified and redundant transcripts were removed. Quality filtered reads were aligned to the reference transcriptomes (one for each species), counts were generated from the alignment files, and differential expression analysis was performed with DESeq2 via Kallisto. Up and down-regulated genes (padj<0.1) across both age classes (juvenile vs adult) were observed in each species and compared.

opencc-by-4.0Sep 2021View details →