Find research datasets worth reusing

opencc-by-4.0Sep 2021View details →

Expression and Purification of Full-Length T-box Transcription Factor TBXTA-c027

A detailed protocol for the expression and purification of G177D variant of biotinylated, full-length TBXT

opencc-by-4.0Sep 2021View details →

Supplementary data for: Does Phobos reflect solar wind protons? Mars Express special flyby operations with and without the presence of Phobos

Supplementary data to reproduce figures for "Does Phobos reflect solar wind protons? Mars Express special flyby operations with and without the presence of Phobos".

opencc-by-sa-4.0Jan 2018View details →

A comprehensive evaluation of module detection methods for gene expression data

A critical step in the analysis of large genome-wide gene expression datasets is the use of module detection methods to group genes into co-expression modules. Because of limitations of classical clustering methods, numerous alternative module detection methods have been proposed, which improve upon clustering by handling co-expression in only a subset of samples, modeling the regulatory network, or allowing overlap between modules. In this study we use known regulatory networks to do a comprehensive and robust evaluation of these different methods. Overall, decomposition methods outperform all other strategies, while we could not find any clear advantages of biclustering and network-inference based approaches.  Using our evaluation workflow, we also investigate several practical aspects of module detection, such as parameter estimation and the use of alternative similarity measures, and conclude with recommendations for the further development of these methods.

opencc-by-4.0Oct 2021View details →

Heightened condition dependent expression of structural colouration in the faces, but not wings, of male and female flies

Data from White et al. (2021): Heightened condition dependent expression of structural colouration in the faces, but not wings, of male and female flies

opencc-by-4.0Oct 2021View details →

Network analysis reveals rare disease signatures across multiple levels of biological organization - Co-expression dataset

The GTEx-derived co-expression data in 38 tissues generated in Buphamalai et.al., Network analysis reveals rare disease signatures across multiple levels of biological organization, Nature Communications 2021. Please see the publication's Methods section for details.

opencc-zeroOct 2021View details →

Relationships between immune gene expression and circulating cytokine levels in wild house mice

1. Quantitative PCR (qPCR) has been commonly used to measure gene expression in a number of research contexts, but the measured RNA concentrations do not always represent the concentrations of active proteins which they encode. This can be due to transcriptional regulation or post-translational modifications, or localisation of immune environments, as can occur during infection. However, in studies using free-living non-model species, such as in ecoimmunological research, qPCR may be the only available option to measure a parameter of interest, and so understanding the quantitative link between gene expression and associated effector protein levels is vital. 2. Here we use qPCR to measure concentrations of RNA from mesenteric lymph node (MLN) and spleen tissue, and multiplex ELISA of blood serum to measure circulating cytokine concentrations in a wild population of a model species, Mus musculus domesticus. 3. Few significant correlations were found between gene expression levels and circulating cytokines of the same immune genes or proteins, or related functional groups. Where significant correlations were observed, these were most frequently within the measured tissue (i.e. the expression levels of genes measured from spleen tissue were more likely to correlate with each other rather than with genes measured from MLN tissue, or with cytokine concentrations measured from blood). 4. Potential reasons for discrepancies between measures, including differences in decay rates and transcriptional regulation networks are discussed. We highlight the relative usefulness of different measures under different research questions, and consider what might be inferred from immune assays.

opencc-by-4.0Aug 2024View details →

Evaluating computational approaches for comparison of protein expression across cancer indications

######################################################################################################## # CPTAC PAN cancer imputed and normalized data  ######################################################################################################## # R Code snippet iBAQ = readRDS("/your path/iBAQ.rds") table(iBAQ$normalized) # CN                No QN         QN             riBAQ           Smooth QN  # 17435640  17435640   17435640   17435640     17435640  library(dplyr) full.qn <- iBAQ %>% filter(normalized=="QN") OV <- full.qn %>% filter(Indication=="OV")%>% filter(Tissue=="Tumor") OV_4genes <- OV[OV$Gene%in% c("CDH6", "FOLR1", "ERBB2", "TACSTD2"),]

opencc-zeroNov 2022View details →

Chronic Ca2+ imaging of cortical neurons with long-term expression of GCaMP-X

Dynamic Ca2+ signals reflect acute changes in membrane excitability and also mediate signaling cascades in chronic processes. In both cases, chronic Ca2+ imaging is often desired but challenged by the cytotoxicity intrinsic to calmodulin (CaM)-based GCaMP, a series of genetically-encoded Ca2+ indicators that have been widely applied. Here, we demonstrate the performance of GCaMP-X in chronic Ca2+ imaging of cortical neurons, where GCaMP-X by design is to eliminate the unwanted interactions between the conventional GCaMP and endogenous (apo)CaM-binding proteins. By expressing in adult mice at high levels over an extended time frame, GCaMP-X showed less damage and improved performance in two-photon imaging of sensory (whisker-deflection) responses or spontaneous Ca2+ fluctuations, in comparison with GCaMP. Chronic Ca2+ imaging of one month or longer was conducted for cultured cortical neurons expressing GCaMP-X, unveiling that spontaneous/local Ca2+ transients progressively developed into autonomous/global Ca2+ oscillations. Along with the morphological indices of neurite length and soma size, the major metrics of oscillatory Ca2+, including rate, amplitude and synchrony were also examined. Dysregulations of both neuritogenesis and Ca2+ oscillations became discernible around 2–3 weeks after virus injection or drug induction to express GCaMP in newborn or mature neurons, which were exacerbated by stronger or prolonged expression of GCaMP. In contrast, neurons expressing GCaMP-X were significantly less damaged or perturbed, altogether highlighting the unique importance of oscillatory Ca2+ to neural development and neuronal health. In summary, GCaMP-X provides a viable solution for Ca2+ imaging applications involving long-time and/or high-level expression of Ca2+ probes.

opencc-by-4.0Nov 2022View details →

Stereo-seq E12.5_E1S3 bin 200 expression matrix (dgC Matrix), spatial locations (.csv), and h5ad file (scanpy flavor)

Expression matrix in rds file format and spatial locations of E12.5_E1S3 downloaded from the Mouse Organogenesis Spatiotemporal Transcriptomic Atlas. Files were processed using an adapted version of the STOMICS Analysis Workflow (SAW) pipeline.

opencc-by-4.0Nov 2022View details →

Supplementary materials for "SPAG9 expression predicts a good prognosis in patients with clear cell renal cell carcinoma: A bioinformatics integrative analysis"

Supplementary materials for "SPAG9 expression predicts a good prognosis in patients with clear cell renal cell carcinoma: A bioinformatics integrative analysis".

opencc-by-4.0Nov 2022View details →

Saved model and preprocessed data for "CRMnet:a deep learning model for predicting gene expression from large regulatory sequence datasets"

Saved TUNet model and preprocessed training data for "CRMnet: a deep learning model for predicting gene expression from large regulatory sequence datasets" To load the trained model: <pre><code class="language-python">import tensorflow as tf tf.keras.models.load_model("path to the model folder")</code></pre> for more information please find our repository: https://github.com/jiayuwen/CRMnet

The maternal effects of dietary restriction on Dnmt expression and reproduction in two clones of Daphnia pulex

The inheritance of epigenetic marks induced by environmental variation in a previous generation is broadly accepted as a mediator of phenotypic plasticity. Transgenerational effects linking maternal experiences to changes in morphology, gene expression, and life history of successive generations are known across many taxa. While the number of studies linking epigenetic variation to ecological maternal effects is increasing rapidly, few if any attempts have been made to investigate molecular mechanisms governing epigenetic functions in the context of ecologically relevant maternal effects. Daphnia make an ideal model for investigating molecular epigenetic mechanisms and ecological maternal effects because they will reproduce asexually in the lab. Daphnia are also known to have strong maternal effects, involving a variety of traits and environmental variables. Using two clones of Daphnia pulex, we investigated the plasticity of life history and DNA methyltransferase (Dnmt) gene expression with respect to food limitation within- and across-generations. We found strong evidence of genotypic variation of responses of life history and Dnmt expression to low food diets, both within- and across-generations. In general, effects of offspring diet were larger than either the direct maternal effect or offspring-maternal environment interactions, but the direction of the maternal effect was usually in the opposite direction of the within-generation effect. For both life history and Dnmt expression, we also found that when offspring had low food, effects of the maternal environment were stronger than when offspring had high food.

opencc-by-4.0Dec 2022View details →

Exercise training prior to manifestation of hypertrophic cardiomyopathy in mice attenuates expression of pro-fibrotic genes - supplementary information

Supplementary data for research article titled "Exercise training prior to manifestation of hypertrophic cardiomyopathy in mice attenuates expression of pro-fibrotic genes"

Foraging behaviour variations, for gene expression and transcriptomic divergence in parasitic wasp populations of Venturia canescens

Foraging behaviours encompass strategies to locate resources and to exploit them. In many taxa, these behaviours are driven by a major gene called for, but mechanisms vary between species. In the parasitoid wasp Venturia canescens, sexual and asexual populations coexist in sympatry but differ in life-history trait, physiology and behaviours, which could impact their foraging strategies. Here, we explored the molecular bases underpinning divergence in behaviours by testing two mutually nonexclusive hypotheses: first, the divergence in the for gene correlates with difference in foraging strategies, and second, the latter rely on a divergence in whole-genome expression. Using comparative genomics, we showed that the for gene was conserved across insects considering both sequence and gene model complexity. Polymorphism analysis did not support the occurrence of two allelic variants diverging across the two populations, yet the asexual population exhibited less polymorphism than the sexual population. Sexual and asexual transcriptomes sharply split, with 10.9% of differentially expressed genes, but these were not enriched in behavioural-related genes. We showed that the for gene was more highly expressed in asexual female heads than in sexual heads and that those differences correlate with divergence in foraging behaviours in our experiment since asexuals explored the environment more and exploited more host patches. Overall, these results suggested that fine tuning of for gene expression between populations may have led to distinct foraging behaviours. We hypothesized that reproductive polymorphism and coexistence in sympatry of sexual and asexual populations specialized to different ecological niches via divergent optima on phenotypic traits could imply adaptation through different expression patterns of the for gene and at many other loci throughout the genome.

opencc-by-4.0Dec 2022View details →

Gene expression responses of Bactrocera tryoni larvae feeding on different ripening stages of tomato fruit

Bactrocera tryoni larvae rearing in immature-green, color-break, and fully-ripe tomato fruit's RSEM, DGE, Trinity Fasta file, Trinity Fasta gene to transcript map, and Trinotate annotation report data.

Data for: Self-cleaving 2A peptides allow for expression of multiple genes in Dictyostelium discoideum

The social amoeba Dictyostelium discoideum is a model for a wide range of biological processes including chemotaxis, cell-cell communication, phagocytosis, and development. Interrogating these processes with modern genetic tools often requires the expression of multiple transgenes. While it is possible to transfect multiple transcriptional units, the use of separate promoters and terminators for each gene leads to large plasmid sizes and possible interference between units. In many eukaryotic systems this challenge has been addressed through polycistronic expression mediated by 2A viral peptides, permitting efficient, co-regulated gene expression. Here, we screen the most commonly used 2A peptides, porcine teschovirus-1 2A (P2A), Thosea asigna virus 2A (T2A), equine rhinitis A virus 2A (E2A), and foot-and-mouth disease virus 2A (F2A), for activity in D. discoideum and find that all the screened 2A sequences are effective. However, combining the coding sequences of two proteins into a single transcript leads to notable strain-dependent decreases in expression level, suggesting additional factors regulate gene expression in D. discoideum that merit further investigation. Our results show that P2A is the optimal sequence for polycistronic expression in D. discoideum, opening up new possibilities for genetic engineering in this model system.

Effects of ACTH4-10Pro8-Gly9-Pro10 on anti-inflammatory cytokine (IL-4, IL-10, IL-13) expression in acute spinal cord injury model (Sprague Dawley rats)

Background: Spinal cord injury (SCI) is a destructive neurological and pathological state that causes major motor, sensory and autonomic dysfunctions. It's final neurological outcome determined from both primary and secondary injury process. Neuroinflammation is a key component of the secondary injury mechanisms with local and systemic consequences. A neuroprotective compound, ACTH4-10Pro8-Gly9-Pro10 also known as Semax has shown neuroprotective and anti-inflammatory properties. ACTH4-10Pro8-Gly9-Pro10 also has actively used in the treatment of brain ischemia without serious complication reported. Here we analyzed the effects of ACTH4-10Pro8-Gly9-Pro10 in regulating inflammatory cascade in SCI by looking at the expression of anti-inflammatory cytokine IL-4, IL-10, IL-13 in acute compression SCI. Method: We do laminectomy in Sprague Dawley rats at the second thoracic vertebrae. After laminectomy we expose the myelum and create mild SCI model with 20gr and severe SCI with 35gr aneurysm clips. ACTH4-10Pro8-Gly9-Pro10 was administered intranasally to the treatment group and 0,9% NaCl to the control group (placebo). Both group was remain alive and terminated at 3 and 6 hour. The preparations tissue sample were fixed in formalin and examined for immunohistochemistry. Quantitative measurement of anti-inflammatory cytokine (IL-4, IL-10, IL-13) was done in posterior horn with associated anti-monoclonal antibodies. Result: Rats with mild SCI that were given ACTH4-10Pro8-Gly9-Pro10 shown greater expression of IL-4, IL-10 and IL-13 at three hour post compression but only IL-10 and IL-13 elevated significantly at six hour. Rats with severe compression in ACTH4-10Pro8-Gly9-Pro10 group shown greater expression of IL-10, IL-13 at three hour and IL-4, IL-10 at six hour compared with the placebo group. Conclusion: Administration of ACTH4-10Pro8-Gly9-Pro10 intranasal can increase anti inflammatory cytokine expression at Sprague Dawley rat model with mild and severe SCI. Expression of anti inflammatory cytokine was greater in mild compression and early hour (3 hour). Further research needs to be done to determine optimal dose and the actual clinical outcome in vivo.

opencc-by-4.0Feb 2023View details →

Androgen and prolactin manipulation do not induce changes in gene expression in the telencephalon in parental male bluegill (Lepomis macrochirus) during parental care

Transcriptome of the prosencephalon of 11-KT, prolactin and placebo implanted fish.

opencc-zeroJan 2023View details →

Disturbing the spatial structure of biofilms affects the expression of agr regulated virulence factors in Staphylococcus aureus

Staphylococcus aureus uses quorum sensing and nutrient availability to control the expression of agr-regulated virulence factors. Quorum sensing is mediated by autoinducing peptide (AIP), which at high concentration, reduces expression of surface attachment proteins (coa, fnbpA), and increases expression of exotoxins (lukS) and proteases (splA). Nutrient availability can be sensed through the saeS/saeR system. Low nutrients increase expression of saeR, which augments expression of coa and fnbpA distinct from AIP. The formation of spatial structure, such as biofilms, can alter quorum sensing and nutrient acquisition. In natural environments, biofilms encounter forces that may alter their spatial structure. This may impact quorum sensing and/or nutrient acquisition, and thus affect the expression of agr-regulated virulence factors. However, this has not been studied. We show that periodically disturbing biofilms composed of S. aureus using a physical force affects the expression of agr-regulated virulence factors. In nutrient-poor environments, disturbance increased the expression of coa, fnbpA, lukS, and splA. Disturbance into a nutrient-rich environment at low or high disturbance amplitudes moderately reduced expression of coa and fnbpA but increased expression of lukS and splA. Interestingly, at an intermediate amplitude, the overall expression of agr-regulated virulence factors was the lowest; expression of lukS and splA remained unchanged relative to an undisturbed biofilm while expression of coa and fnbpA significantly decreased. We hypothesize that these changes are a result of disturbance-driven changes in access to AIP and nutrients. Our results may allow the identification of environments where virulence is enhanced, or reduced, owing to disturbance.