Find research datasets worth reusing

opencc-zeroDec 2017View details →

Data from: Type 1 interferon-inducible gene expression in QuantiFERON Gold TB-positive uveitis: a tool to stratify a high versus low risk of active tuberculosis?

QuantiFERON-Gold TB (QFT)-positive patients with undetermined cause of uveitis are problematic in terms of whether to diagnose and treat them for tuberculosis (TB). Here, we investigated whether peripheral blood expression of type 1 interferon (IFN)-inducible genes may be of use to stratify QFT-positive patients with uveitis into groups of high versus low risk of having active TB-associated uveitis. We recruited all new uveitis patients in Cipto Mangunkusumo Hospital, Jakarta, Indonesia for one year. We included 12 patients with uveitis and clinically diagnosed active pulmonary TB, 58 QFT-positive patients with uveitis of unknown cause, 10 newly diagnosed sputum-positive active pulmonary TB patients without uveitis and 23 QFT-negative healthy controls. Expression of 35 type 1 IFN-inducible genes was measured in peripheral blood cells from active pulmonary TB patients without uveitis and healthy controls. Differentially expressed genes were identified and used for further clustering analyses of the uveitis groups. A type-1 IFN gene signature score was calculated and the optimal cut-off value for this score to differentiate active pulmonary TB from healthy controls was determined and applied to QFT-positive patients with uveitis of unknown cause. Ten type 1 IFN-inducible genes were differentially expressed between active pulmonary TB and healthy controls. Expression of these 10 genes in QFT-positive patients with uveitis of unknown cause revealed three groups: 1); patients resembling active pulmonary TB, 2); patients resembling healthy controls, and 3); patients displaying an in-between gene expression pattern. A type 1 IFN gene signature score ≥5.61 displayed high sensitivity (100%) and specificity (91%) for identification of active TB. Application of this score to QFT-positive patients with uveitis of unknown cause yielded two groups with expected different likelihood (high vs. low) of having active-TB uveitis, and therefore may be useful in clinical management decisions.

opencc-zeroDec 2013View details →

Data from: Premating isolation is determined by larval rearing substrates in cactophilic Drosophila mojavensis. X. Age-specific dynamics of adult epicuticular hyrdocarbon expression in response to different host plants

Analysis of sexual selection and sexual isolation in Drosophila mojavensis and its relatives has revealed a pervasive role of rearing substrates on adult courtship behavior when flies were reared on fermenting cactus in preadult stages. Here, we assessed expression of contact pheromones comprised of epicuticular hydrocarbons (CHCs) from eclosion to 28 days of age in adults from two populations reared on fermenting tissues of two host cacti over the entire life cycle. Flies were never exposed to laboratory food and showed significant reductions in average CHC amounts consistent with CHCs of wild-caught flies. Overall, total hydrocarbon amounts increased from eclosion to 14–18 days, well past age at sexual maturity, and then declined in older flies. Most flies did not survive past 4 weeks. Baja California and mainland populations showed significantly different age-specific CHC profiles where Baja adults showed far less age-specific changes in CHC expression. Adults from populations reared on the host cactus typically used in nature expressed more CHCs than on the alternate host. MANCOVA with age as the covariate for the first six CHC principal components showed extensive differences in CHC composition due to age, population, cactus, sex, and age × population, age × sex, and age × cactus interactions. Thus, understanding variation in CHC composition as adult D. mojavensis age requires information about population and host plant differences, with potential influences on patterns of mate choice, sexual selection, and sexual isolation, and ultimately how these pheromones are expressed in natural populations. Studies of drosophilid aging in the wild are badly needed.

opencc-zeroDec 2017View details →

Data from: Despite high levels of expression in thymic epithelial cells, miR-181a1 and miR-181b1 are not required for thymic development

MicroRNAs (miRNAs) have been shown to be key modulators of post-transcriptional gene silencing in many cellular processes. In previous studies designed to understand the role of miRNAs in thymic development, we globally deleted miRNA exclusively in thymic epithelial cells (TECs), which are critical in thymic selection. This resulted in the loss of stromal cells that instruct T cell lineage commitment and affect thymocyte positive selection, required for mature T cell development. Since murine miR-181 is expressed in the thymus and miR-181 deficiency disrupts thymocyte development, we first quantified and thereby demonstrated that miR181a1 and miR181b1 are expressed in purified TECs. By generating mice with TEC targeted loss of miR-181a1 and miR-181b1 expression, we observed that neither TEC cellularity nor thymocyte number nor differentiation was adversely affected. Thus, disrupted thymopoiesis in miR-181 deficient mice was not due to miR-181 loss of expression in TECs. Importantly, in mice with restricted TEC deficiency of miR-181a1 and miR-181b1, there were similar numbers of mature T cells in the periphery in regards to frequencies, differentiation, and function as compared to controls. Moreover miR-181a1 and miR-181b1 were not required for maintenance of thymus integrity over time, as thymic involution was not accelerated in gene-targeted mice. Taken together our data indicate that miR-181a1 and miR-181b1 are dispensable for TEC differentiation, their control of thymocyte development and mature T cell export to and homeostasis within the periphery.

opencc-by-4.0Jun 2022View details →

Data of FigS1, "The Potential Tumor-Suppressor DHRS7 Inversely Correlates with EGFR Expression in Prostate Cancer Cells and Tumor Samples"

Data of FigS1, “The Potential Tumor-Suppressor DHRS7 Inversely Correlates with EGFR Expression in Prostate Cancer Cells and Tumor Samples” The Dataset (original publication: doi: 10.3390/cancers14133074) contains the original figure as PNG-format (10.3390-cancers14133074_FigS1.PNG). The Corresponding raw data and subsequent data analysis obtained for TCGA analysis contains three files in csv-format (31003A-179400_10.3390-cancers14133074_SSDHRS7_23_2-1-3 .csv), three files in sps-format (31003A-179400_10.3390-cancers14133074_SSDHRS7_23_2-1-3 .sps), all further related information provided as one meta-data-file in pdf-format (31003A-179400_10.3390-cancers14133074_SSDHRS7_23_2_M1.pdf)  and one in txt-format (31003A-179400_10.3390-cancers14133074_SSDHRS7_23_2_M.txt).

opencc-zeroJul 2022View details →

Rational domestication of a plant-based recombinant expression system expands its biosynthetic range

Plant molecular farming aims to provide a green, flexible, and rapid alternative to conventional recombinant expression systems, capable of producing complex biologics such as enzymes, vaccines, and antibodies. Historically, the recombinant expression of therapeutic peptides in plants has proven difficult, largely due to their small size and instability. However, some plant species harbour the capacity for peptide backbone cyclization, a feature inherent in stable therapeutic peptides. One obstacle to realizing the potential of plant-based therapeutic peptide production is the proteolysis of the precursor before it is matured into its final stabilized form. Here we demonstrate the rational domestication of Nicotiana benthamiana within two generations to endow this plant molecular farming host with an expanded repertoire of peptide sequence space. The in planta production of molecules including an insecticidal peptide, a prostate cancer therapeutic lead and an orally active analgesic are demonstrated.

opencc-zeroJul 2022View details →

Habitat change alters the expression and efficiency of a female ornament

Anthropogenic habitat changes are disrupting the mate choice process in a range of organisms, with consequences for populations and communities. Research has so far focussed on male sexually selected traits and female mate choice, given their conspicuousness, while effects on female ornaments and male mate choice have been largely overlooked. Yet, females of many species develop ornaments that males use in mate choice. These ornaments can be costly and reduce female fecundity and viability and, hence, influence population growth rate. Thus, attention should be paid to changes in these ornaments and the consequences the changes have for populations. Here, we show that declining visibility in aquatic ecosystems reduces the investment of female threespine stickleback in a melanin-based ornament in favour of increased search activity. The adjustment appears adaptive as males pay less attention to the ornament under poor visibility, and as melanin-based ornaments are physiologically costly. It is likely that past fluctuations in visibility has promoted the evolution of environment-dependent plasticity in female ornamentation. More attention should be paid to changes in female ornaments and their adaptive value, across taxa, given the impact that female investment in ornaments can have on fecundity and population growth rate. Environments are changing at an accelerating rate because of human activities and knowledge of the responses of both males and females to these changes are needed to evaluate and predict the ultimate impact on populations and biodiversity. Keywords: environmental change, eutrophication, fecundity, reproduction, sexual selection, signals

opencc-zeroAug 2022View details →

The effect of dietary supplementation with blueberry, cyanidin-3-O-β-glucoside, yoghurt and its peptides on gene expression associated with glucose metabolism in skeletal muscle obtained from a high-fat-high-carbohydrate diet induced obesity model

Obesity is a leading global health problem contributing to various chronic diseases, including type II diabetes mellitus (T2DM). The aim of this study was to investigate whether blueberries, yoghurt, and their respective bioactive components, Cyanidin-3-O-β-glucoside (C3G) and peptides alone or in combinations, alter the expression of genes related to glucose metabolism in skeletal muscles from diet-induced obese mice. In extensor digitorum longus (EDL), yoghurt up-regulated the expression of activation of 5'adenosine monophosphate-activated protein kinase (AMPK), insulin receptor substrate-1 (IRS-1), phosphatidylinositol-3 kinase (PI3K) and glucose transporter 4 (GLUT4), and down-regulated the expression of angiotensin II receptor type 1 (AGTR-1). The combination of blueberries and yoghurt down-regulated the mRNA expression of AGTR-1 and Forkhead box protein O1 (FoxO1) in the EDL. Whereas the combination of C3G and peptides down-regulated AGTR-1 and up-regulated GLUT4 mRNA expression in the EDL. In the soleus, blueberries and yoghurt alone, and their combination down-regulated AGTR-1 and up-regulated GLUT4 mRNA expression. In summary blueberries and yoghurt, regulated multiple genes associated with glucose metabolism in skeletal muscles, and therefore may play a role in the management and prevention of T2DM.

opencc-by-4.0Aug 2022View details →

Bacterial RNA Virus MS2 Exposure Increases the Expression of Cancer Progression genes in LNCaP Prostate Cancer Cell Line

Supplementary Figure 1. Network of protein-protein interactions in LNCaP cells according to their interaction with T4 and M13 phages (DNA phages). The network of protein-protein interactions in Homo Sapiens was constructed using the string protein-protein interaction network v 11.5 [35] with the overexpressed genes (highest confidence level setting) in LNCaP cells. Interactions of overexpressed protein genes were mapped with the highest confidence cut-off of (0.7-0.9). In the resulting protein association network, proteins are presented as nodes connected by lines with varying thicknesses representing the highest confidence level of (0.7-0.9). It is observed that there is strong experimentally determining evidence for the link between SRC and other overexpressed genes, including MAPKs and other integrins by adding more nodes until the highest confidence level of (0.7-0.9) among all overexpressed genes was obtained based on known interactions.   Supplementary Figure 2. Enrichr web server-based gene set enrichment analysis for overexpressed cancer progression genes in LNCaP cells treated with (A) MS2 and (B) T4 and M13 phages; which predicts caveolin-mediated endocytosis for MS2 bacterial virus (with a p-value of 0.000001399). Similarly, an integrin-mediated signaling pathway (with a p-value of 0.000007588) based on overexpression of most integrin genes and caveolin-mediated endocytosis (with a p-value of 0.000001799) were predicted for both T4 and M13 phages based on GO Biological process 2021.

opencc-by-4.0Sep 2022View details →

Efficient gene expression in human stem cell derived-cortical organoids using adeno associated virus

Supplementary figure 6. Neuronal network activity in human cortical organoid. Videos of AAV-mediated expression of the calcium indicator jGCaMP7 under the human synapsin promoter for control (aCSF), glutamate, gabazine and TTX treated cortical organoids.

opencc-by-4.0Mar 2021View details →

Gene expression and splicing counts from the Yepez, Gusic et al study - strand-specific

File description: <ol> <li> geneCounts: gene-level counts  </li> <li> k_j: split counts spanning from one exon to another. </li> <li> k_theta: non-split counts covering a splice site </li> <li> n_psi3: total split counts from a given acceptor site </li> <li> n_psi5: total split counts from a given donor site </li> <li> n_theta: total split and non-split counts for a given splice site </li> <li> Sample annotation describing each sample from the dataset </li> <li> Description file with global information from the dataset </li> </ol>   The gene counts were originated using the GTF file from release 34 of GENCODE <a href="https://www.gencodegenes.org/human/release_34">https://www.gencodegenes.org/human/release_34</a>, and the split and non-split counts contain only the annotated junctions from the same release. Use: The count matrices are intended to help researchers that are interested in using RNA-Seq data with the purpose of diagnostics. Researchers can merge their own dataset with the downloaded ones, provided the tissue, genome build, strand, and paired-end specifications match. Afterwards, DROP can be used to compute expression and splicing outliers (<a href="https://github.com/gagneurlab/drop">https://github.com/gagneurlab/drop</a>). Number of samples: 269 Tissue: Fibroblast Organism: Homo sapiens Genome assembly: hg19 Gene annotation: gencode34 Disease (ICD-10: N): E72: 4, E75: 2, E77: 1, E88: 199, F82: 1, F89: 7, G31: 14, G40: 2, G71: 3, G82: 1, G93: 2, I42: 1, K72: 4, NONE: 18, P94: 2, Q02: 1, Q78: 1, R16: 2, R27: 3, R29: 1 Strand specific: TRUE Paired end: TRUE Protocol: poly(A) enrichment Dataset contact: Vicente Yepez, yepez@in.tum.de; Julien Gagneur, gagneur@in.tum.de; Holger Prokisch, prokisch@helmholtz-muenchen.de Citation: Cite both the resource using Zenodo's citation and the publication under References

PDE12 expression data from diabetes patients and controls

Type 1 diabetes (T1D) incidence is increased after COVID-19 infection in children under 18 years of age. Interferon-α-activated oligoadenylate synthetase and downstream RNAseL activation degrade pathogen RNA, but can also damage host RNA when RNAseL activity is poorly regulated. One such regulator is PDE12 which degrades 2′-5′ oligoadenylate units, thereby decreasing RNAseL activity. We analyzed PDE12 expression in islets from non-diabetic donors, individuals with newly (median disease duration 35 days) and recently (5 years) diagnosed T1D, and individuals with type 2 diabetes (T2D). We also analyzed PDE12 single-nucleotide polymorphisms (SNPs) relative to T1D incidence. PDE12 expression was decreased in individuals with recently diagnosed T1D, in three of five individuals with newly diagnosed T1D, but not in individuals with T2D. Two rare PDE12 SNPs were found to have odds ratios of 1.80 and 1.74 for T1D development. We discuss whether decreased PDE12 expression after COVID-19 infection might be part of the up to 2.5-fold increase in T1D incidence.

opencc-by-4.0Oct 2022View details →

Transcription factor expression is the main determinant of variability in gene co-activity

Summary Co-activity scores for 343 GEUVADIS LCLs and ABC scores for 68 LCLs, of which 30 are contained in both. Project abstract Many genes are co-regulated and, when proximal, form domains of coordinated gene activity. However, the regulatory determinants of domain co-activity remain unclear. Here, we leverage human individual variation in gene expression to characterize the regulatory processes underlying the activities of such domains and systematically quantify their effect sizes. We employ transcriptional decomposition to extract from RNA expression data an expression component related to co-activity revealed by genomic positioning. This strategy reveals close to 1,500 domains of co-activity, covering most expressed genes, of which the large majority are invariable across individuals. Focusing specifically on domains with high variation in co-activity reveals that neighboring genes contained within variable co-activity domains have a higher sharing of eQTLs, a higher variability in enhancer interactions, and a specific enrichment of binding by variably expressed transcription factors. Through careful quantification of the relative contributions of regulatory activities underlying co-activity, we find transcription factor expression levels to be the main determinant of gene co-activity, indicating that distal trans effects contribute more than local genetic variation to individual variation in co-activity domains.  Included files Co_activity_scores_343_individuals.tsv.zip - Contains co-activity scores for included individuals. Columns include chromosome, bin, start, end and one column per individual containing the co-activity score. ABC_scores_68_individuals.tsv.zip - Contains ABC scores for included individuals. Columns include chromosome, start of putative enhancer region, end of putative enhancer region, name of putative enhancer region, target gene, TSS of target gene, LCL identifier, ABC score

Heat shock protein gene expression varies among tissues and populations in free living birds

Climate change is dramatically altering our planet, yet our understanding of mechanisms of thermal tolerance is limited in wild birds. We characterized natural variation in heat shock protein (HSP) gene expression among tissues and populations of free-living Tree Swallows (Tachycineta bicolor). We focused on HSPs because they prevent cellular damage and promote recovery from heat stress. We used quantitative PCR to measure gene expression of three HSPs, including those in the HSP70 and HSP90 families that have robust experimental connections to heat in past literature. First, to evaluate how tissues and, by extension, the functions that they mediate, may vary in their thermal protection, we compared HSP gene expression among neural and peripheral tissues. We hypothesized that tissues with particularly vital functions would be more protected from heat as indicated by higher HSP gene expression. We found that brain tissues had consistently higher HSP gene expression compared to the pectoral muscle. Next, we compared HSP gene expression across four distinct populations that span over 20 degrees of latitude (>2300 km). We hypothesized that the more southern populations would have higher HSP gene expression, suggesting greater tolerance of, or experience with, warmer local conditions. We observed largely higher HSP gene expression in more southern populations than northern populations, although this pattern was more striking at the extremes (southern Indiana vs. Alaska) and it was stronger in some brain areas than others (ventromedial telencephalon vs. hypothalamus). These results shed light on the potential mechanisms that may underlie thermal tolerance differences among populations or among tissues.

opencc-by-4.0Oct 2022View details →

RNA-Seq data of Raji cells transduced with retrovirus expressing WT or mutant IRF4

Total RNA was extracted using RNAiso Plus (TaKaRa) from Raji cells transduced with retrovirus expressing WT or mutant IRF4. RNA-seq was performed by BGI (Beijing Genomic Institute, ShenZhen, China) using the BGISEQ-500 platform, pair end 100 bases read lengths. The sequencing data were filtered with SOAPnuke (v1.5.2). The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to identify genes and differentially spliced genes (DSGs), respectively. Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database for this organism built by BGI with known and novel coding transcripts included, then the expression level of gene was calculated by RSEM (v1.2.12).

Zbtb14 regulates monocyte and macrophage development through inhibiting pu.1 expression in zebrafish

To elucidate the mechanism underlying the aberrant monocyte/macrophage development of zbtb14-/- mutant, GFP-positive cells were isolated from either wild-type Tg(mpeg1.1:eGFP) or zbtb14 -/- //Tg(mpeg1.1:eGFP) larvae at 2dpf by FACS. mRNA was extracted from sorted cells using RNeasy Micro (Qiagen, Manchester, UK) and mRNA libraries were constructed using NEBNext Ultra RNA Library Prep Kit for52 Illumina and sequenced under Illumina HiSeq X Ten with pair end 150bp (PE150).

Data for: Differentially expressed genes comparing WT plants vs xal1-2

The balance between cell proliferation, differentiation, and elongation rates emerge from regulatory gene differentiation networks coupled to various signal transduction pathways, including those of reactive oxygen species (ROS). The Arabidopsis thaliana primary root has become a useful system to unravel such networks, as well as their interaction with signals that alter organ growth. The role of transcription factors, that regulate organ development, in mediating the role of ROS in root growth is just beginning to be studied. Here, we report that the MADS-box transcription factor XAANTAL1 (XAL1) mediates hydrogen peroxide (H2O2) role in primary root growth and it is involved in the morphogenesis of the columella stem cell differentiation in response to H2O2. Interestingly, our data suggest that XAL1 is a positive regulator of H2O2 concentration in the root meristem via regulating transcript accumulation of several peroxidases. Moreover, we found that XAL1 is necessary for the H2O2-induced inhibition of primary root growth through the negative regulation activities of the peroxidases and catalases. Furthermore, XAL1 and RETINOBLASTOMA-RELATED (RBR) are also necessary to positively regulate columella stem cell differentiation that is triggered by moderate H2O2 treatments.

DUX4 expression activates JNK and p38 MAP kinases in myoblasts: MAJIQ splicing results

Facioscapulohumoral muscular dystrophy (FSHD) is caused by misexpression of the DUX4 transcription factor in skeletal muscle that results in transcriptional alterations, abnormal phenotypes, and cell death. To gain insight into the kinetics of DUX4-induced stresses, we activated DUX4 expression in myoblasts and performed longitudinal RNA sequencing (GEO GSE205421) paired with proteomics and phosphoproteomics (MassIVE MSV000089812). This analysis revealed changes in cellular physiology including DNA damage and altered mRNA splicing. Phosphoproteomic analysis uncovered widespread changes in protein phosphorylation rapidly following DUX4 induction indicating that alterations in kinase signaling may play a role in DUX4-mediated stress and cell death. Indeed, we demonstrate that two stress-responsive MAP kinase pathways, JNK and p38, are activated in response to DUX4 expression. Inhibition of each of these pathways ameliorated DUX4-mediated cell death in myoblasts. These findings uncover JNK as a novel pathway involved in DUX4-mediated cell death as well as provide additional insights into the role of the p38 pathway, a clinical target for the treatment of FSHD.

opencc-byMar 2022View details →

NoEndOf Express

NoEndOf Express Train Company badge (fictional company). Source: Objaverse 1.0 / Sketchfab

opencc-by-4.0Oct 2017View details →

Expression and purification of Huntingtin interaction protein High mobility group protein B1 (HMGB1) – 2017/10/04

Huntingtin structure function open lab notebook project.