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opencc-zeroDec 2021View details →

OPT data from: A novel cis-regulatory element drives early expression of Nkx3.2 in the gnathostome primary jaw joint

The acquisition of movable jaws was a major event during vertebrate evolution. The role of NK3 homeobox 2 (Nkx3.2) transcription factor in patterning the primary jaw joint of gnathostomes (jawed vertebrates) is well known, however, knowledge about its regulatory mechanism is lacking. In this study, we report a proximal enhancer element of Nkx3.2 that is deeply conserved in most gnathostomes but undetectable in the jawless hagfish and lamprey. This enhancer is active in the developing jaw joint region of the zebrafish Danio rerio, and was thus designated as jaw joint regulatory sequence 1 (JRS1). We further show that JRS1 enhancer sequences from a range of gnathostome species, including a chondrichthyan and mammals, have the same activity in the jaw joint as the native zebrafish enhancer, indicating a high degree of functional conservation despite the divergence of cartilaginous and bony fish lineages or the transition of the primary jaw joint into the middle ear of mammals. Finally, we show that deletion of JRS1 from the zebrafish genome using CRISPR/Cas9 results in a significant reduction of early gene expression of Nkx3.2 and leads to transient jaw joint deformation and partial fusion. The emergence of this Nkx3.2 enhancer in early gnathostomes may have contributed to the origin and shaping of the articulating surfaces of vertebrate jaws.

Mutation and methylation data for study: Assessment of the molecular heterogeneity of E-cadherin expression in invasive lobular breast cancer

Processed mutation data and DNA methylation beta values published with this study.

Expression and function of Twitch-2B in the granulosa cells of mouse ovarian follicles

Briefly, antral follicles were dissected from 23- to 26-d-old RR8; Bact_Cre mice. Follicles were cultured for 24–30 h on organotypic membranes (Millipore; cat. No. PICMORG50) in the presence of follicle-stimulating hormone. The follicle was held in a perfusion slide consisting of a plastic slide (ibidi) and a glass coverslip and assembled using silicon grease. The slide was constructed such that medium containing ovine LH (National Hormone and Peptide Program; 10 μg/mL) could be perfused through a 200-μm-deep channel holding the follicle. Temperature was maintained at 30–34 °C, by use of a warm air blower (Nevtek). Preovulatory Follicles were imaged using a Zeiss Pascal confocal microscope with a 40X/1.2 NA objective. Images were collected every 10 seconds. Measurements were corrected for autofluorescence and for spectral bleed-through of CFP into the YFP channel. Ratios were calculated by dividing the mean CFP intensity in each region of interest by the mean YFP intensity. Data analysis was done using ImageJ and Excel software. Data is representative of 4 follicles.

Supplementary materials for "Integration of public DNA methylation and expression networks via eQTMs improves prediction of functional gene–gene associations"

This repository contained supplementary materials in the study named: "Integration of public DNA methylation and expression networks via eQTMs improves prediction of functional gene–gene associations." For extracting all files from the downloaded tar.gz file, the following commanda could be used: <pre><code>tar -xf supplementary_materials.tar.gz </code></pre> The supplementary_materials/data diretcory contains the following sections: <ol> <li>eqtm_predictions: This contains the training and testing datasets for the eQTM prediction procedures</li> <li>public_methylation_data_and_pca: This contains the harmonized public DNA methylation dataset and its first 100 PCA components</li> <li>cca_data: This contains the CCA components for the public DNA methylation and gene expression datasets for the negative eQTMs, and the input datasets for the functional gene pair prediction analylsis.</li> <li>gene_enrichment_results_for_cca: This contains the gene enrichment results for the CCA components for negative and positive eQTMs</li> </ol> The supplementary_materials/model directory contains the following sections: <ol> <li>disease_tissue_predictions: This contains the models trained for tissue prediction and disease prediction based on the PCA components from the public DNA methylation data</li> <li>eqtm_predictions: This contains models trained for eQTM prediction</li> <li>cca_transformations: This contains CCA transformation models and models for STRING gene pair predictions  </li> </ol>

opencc-zeroDec 2021View details →

Condition dependent seminal fluid gene expression and intergenerational paternal effects on ejaculate quality

1. There is increasing evidence to show that the environment experienced by fathers can have intergenerational paternal effects on the phenotype of offspring. Paternal effects can be mediated by ejaculate traits beyond the genes carried by sperm, for example through methylation of DNA during spermatogenesis, or non-sperm components of the ejaculate such as small RNAs or seminal fluid proteins (sfp). 2. Theory suggests that ejaculate-mediated paternal effects can have important evolutionary consequences, especially if they exhibit condition dependent expression. Here we use the nutritional geometry approach to explore condition dependence in ejaculate traits and intergenerational paternal effects in the cricket Teleogryllus oceanicus. 3. We fed males one of 24 chemically defined diets that varied in macronutrient concentration and the ratio of protein (P) to carbohydrate (C). We measured paternal expenditure on testes and accessory gland growth, and the expression of three seminal fluid protein genes that are known to impact sperm viability and the survival of embryos to hatching. We also measured the hatching success and reproductive phenotypes of adult offspring. 4. We found linear effects of P and C on testes and accessory gland mass, and linear and correlated effects of P and C on the expression of two sfp genes. Paternal diet had no effect on the survival of embryos to hatching. 5. There were significant intergenerational effects of paternal diet on the viability of sperm produced by sons, but no paternal effects on the expression of sfp genes in sons or fecundity in daughters. 6. Our data suggest that ejaculate quality can have a significant non-genetic component determined by the paternal environment, which holds important implications for the evolutionary maintenance of variation in heritable male fitness.

opencc-zeroDec 2021View details →

Mimulus cardinalis plasticity analyses and R scripts for: Spatial variation in high temperature-regulated gene expression predicts evolution of plasticity with climate change in the scarlet monkeyflower

A major way that organisms can adapt to changing environmental conditions is by evolving increased or decreased phenotypic plasticity. In the face of current global warming, more attention is being paid to the role of plasticity in maintaining fitness as abiotic conditions change over time. However, given that temporal data can be challenging to acquire, a major question is whether evolution in plasticity across space can predict adaptive plasticity across time. In growth chambers simulating two thermal regimes, we generated transcriptome data for western North American scarlet monkeyflowers (Mimulus cardinalis) collected from different latitudes and years (2010 and 2017) to test hypotheses about how plasticity in gene expression is responding to increases in temperature, and if this pattern is consistent across time and space. Supporting the genetic compensation hypothesis, individuals whose progenitors were collected from the warmer-origin northern 2017 descendant cohort showed lower thermal plasticity in gene expression than their cooler-origin northern 2010 ancestors. This was largely due to a change in response at the warmer (40ºC) rather than cooler (20ºC) treatment. A similar pattern of reduced plasticity, largely due to a change in response at 40ºC, was also found for the cooler-origin northern versus the warmer-origin southern population from 2017. Our results demonstrate that reduced phenotypic plasticity can evolve with warming and that spatial and temporal changes in plasticity predict one another.

opencc-by-4.0Nov 2021View details →

Projection of high-dimensional genome-wide expression on SOM transcriptome landscapes: supplementary datasets

This is a supplementary dataset with raw data, scripts, and complete analysis results for the paper "Supervised projection of high-dimensional genome-wide expression on SOM transcriptome landscapes".   The archive contains three folders: 1. "Simdata" folder contains data, scripts, and results of performance evaluation of extension SOM and supervised SOM with simulated data.  2. "IBD" - folder contains data, scripts, and results of analysis of Inflammatory bowel disease datasets. 3. "BC" - folder contains data, scripts, and results of analysis of breast cancer datasets.

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-4.0Jan 2022View details →

Expression of CDCA2 in hepatocellular carcinoma by immunohistochemistry and patients' information

Cohort of hepatocellular carcinoma patients enrolled in the study entitled "Cell division cycle associated 2 (CDCA2) upregulation promotes the progression of hepatocellular carcinoma in a p53-dependant mannar". CDCA2 expression in paraffin-embedded liver cancer tissue sections was evaluated by immunohistochemistry. Patients' clinicopathological information was collected.

opencc-by-4.0Jan 2022View details →

A Diagnostic Classifier for Gene Expression-Based Identification of Early Lyme Disease

This data repository contains the source code and pertinent training and test data sets used in the manuscript, A Diagnostic Classifier for Gene Expression-Based Identification of Early Lyme Disease.

Immune disease risk variants regulate gene expression dynamics during CD4+ T cell activation

During activation, T cells undergo extensive changes in gene expression which shape the properties of cells to exert their effector function. Therefore, understanding the genetic regulation of gene expression during T cell activation provides essential insights into how genetic variants influence the response to infections and immune diseases. We generated a single-cell map of expression quantitative trait loci (eQTL) across a T cell activation time-course. We profiled 655,349 CD4+ naive and memory T cells, capturing transcriptional states of unstimulated cells and three time points of cell activation in 119 healthy individuals. We identified 38 cell clusters, including stable clusters such as central and effector memory T cells and transient clusters that were only present at individual time points of activation, such as interferon-responding cells. We mapped eQTLs using a T cell activation trajectory and identified 6,407 eQTL genes, of which a third (2,265 genes) were dynamically regulated during T cell activation. We integrated this information with GWAS variants for immune-mediated diseases and observed 127 colocalizations, with significant enrichment in dynamic eQTLs. Immune disease loci colocalized with genes that are involved in the regulation of T cell activation, and genes with similar functions tended to be perturbed in the same direction by disease risk alleles. Our results emphasize the importance of mapping context-specific gene expression regulation, provide insights into the mechanisms of genetic susceptibility of immune diseases, and help prioritize new therapeutic targets. This dataset comprises of summary stats for eQTLs identified in the study (parquet files) and the ones which passed significance threshold  (tensor_out.tar.gz archive). Files are described by cell subset (CD4 Naive, CD 4 Memory, TEMRA, TCM, etc.), time since activation (16h, 4h, 5days)  as described in the publication (preprint https://doi.org/10.1101/2021.12.06.470953)

Exprimental Data:Caspase-11 non-canonical inflammasome mediates the expression of proinflammatory cytokines in murine macrophages infected with leptospira interrogans.

This is the exprimental data of manuscripts submitted in ALL LIFE magazine. The title is Caspase-11 non-canonical inflammasome mediates the expression of proinflammatory cytokines in murine macrophages infected with leptospira interrogans.)

openother-openFeb 2022View details →

Data and code for "Multi-omics Reveals Microbiome, Host Gene Expression, and Immune Landscape in Gastric Carcinogenesis" by Park et al., iScience 2022

This repository is a part of the supplementary document in Park et al., "Multi-omics Reveals Microbiome, Host Gene Expression, and Immune Landscape in Gastric Carcinogenesis" published in iScience 2022. Abstract: To date, there has been no multi-omic analysis characterizing the intricate relationships between the intragastric microbiome and gastric mucosal gene expression in gastric carcinogenesis. Using multi-omic approaches, we provide a comprehensive view of the connections between the microbiome and host gene expression in distinct stages of gastric carcinogenesis (i.e., healthy, gastritis, cancer). We uncover associations specific to disease states. For example, uniquely in gastritis, Helicobacteraceae is highly correlated with the expression of FAM3D, which has been previously implicated in gastrointestinal inflammation. Additionally, in gastric cancer but not in adjacent gastritis, Lachnospiraceae is highly correlated with the expression of UBD, which regulates mitosis and cell cycle time. Furthermore, lower abundances of B cells in gastric cancer compared to gastritis may suggest a previously unidentified immune evasion process in gastric carcinogenesis. Our integrative analysis provides the most comprehensive description of microbial, host transcriptomic, and immune cell factors of the gastric carcinogenesis pathway.

Gene expression in the lung and liver of SIV-infected macaques.

Analysis of RNA transcripts in the liver and lung of healthy (n=2), SIV infected (n=2) and antiretroviral therapy treated (n=2) rhesus macaques using NovaSeq 6000 flowcell S1 at the Next-Generation Sequencing Platform, Genomics Center (CHU de Québec-Université Laval Research Center, Québec City, Canada). Gene symbols and amounts of transcripts per million (TPM) are listed for each condition.

Raw Data for the article: miRNA expression analysis in the human heart: Undifferentiated progenitors vs. bioptic tissues-Implications for proliferation and ageing

In developed countries, cardiovascular diseases are currently the first cause of death. Cardiospheres (CSs) and cardiosphere-derived cells (CDCs) have been found to have the ability to regenerate the myocardium after myocardial infarction (MI). In recent years, much effort has been made to gain insight into the human heart repair mechanisms, in which miRNAs have been shown to play an important role. In this regard, to elucidate the involvement of miRNAs, we evaluated the miRNA expression profile across human heart biopsy, CSs and CDCs using microarray and next-generation sequencing (NGS) technologies. We identified several miRNAs more represented in the progenitors, where some of them can be responsible for the proliferation or the maintenance of an undifferentiated state, while others have been found to be downregulated in the undifferentiated progenitors compared with the biopsies. Moreover, we also found a correlation between downregulated miRNAs in CSs/CDCs and patient age (eg miR-490) and an inverse correlation among miRNAs upregulated in CSs/CDCs (eg miR-31).

TomExpress_Expression_Table

The manuscript (877959) submitted to Frontiers in Plant Science contains RNA sequencing data. This data is stored in advance of the manuscript's publication in a public, community-supported repository.

Dataset of results for a copper switch for inducing CRISPR/Cas9-based transcriptional activation tightly regulates gene expression in Nicotiana benthamiana.

CRISPR-based programmable transcriptional activators (PTAs) are used in plants for rewiring gene networks. Better tuning of their activity in a time and dose-dependent manner should allow precise control of gene expression. Here, we report the optimization of a Copper Inducible system called CI-switch for conditional gene activation in Nicotiana benthamiana. In the presence of copper, the copper-responsive factor CUP2 undergoes a conformational change and binds a DNA motif named copper-binding site (CBS). In this study, we tested several activation domains fused to CUP2 and found that the non-viral Gal4 domain results in strong activation of a reporter gene equipped with a minimal promoter, offering advantages over previous designs. To connect copper regulation with downstream programmable elements, several copper-dependent configurations of the strong dCasEV2.1 PTA were assayed, aiming at maximizing activation range, while minimizing undesired background expression. The best configuration involved a dual copper regulation of the two protein components of the PTA, namely dCas9:EDLL and MS2:VPR, and a constitutive RNA pol III-driven expression of the third component, a guide RNA with anchoring sites for the MS2 RNA-binding domain. With these optimizations, the CI/dCasEV2.1 system resulted in copper-dependent activation rates of 2,600-fold and 245-fold for the endogenous N. benthamiana DFR and PAL2 genes, respectively, with negligible expression in the absence of the trigger. The tight regulation of copper over CI/dCasEV2.1 makes this system ideal for the conditional production of plant-derived metabolites and recombinant proteins in the field.

opencc-by-4.0Mar 2022View details →

Figures from 'Additional data for the mouse TRPV6 expression atlas'

Figures for the Data in Brief Article 'Additional data for the mouse TRPV6 expression atlas'. Related research article: P. Wartenberg, F. Lux, K. Busch, C. Fecher-Trost, V. Flockerzi, G. Krasteva-Christ, U. Boehm, P. Weissgerber, A TRPV6 expression atlas for the mouse, Cell Calcium, 100 (2021) 102481.

opencc-by-4.0Mar 2022View details →

TagSeq gene expression data from Acropora cervicornis genotypes exhibiting above or below average heat tolerance

TagSeq data taken from Acropora cervicornis genotypes taken from nurseries in the Florida Reef tract and subjected to thermal stress.