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opencc-zeroJan 2023View details →

Arginine-vasopressin expressing neurons in the murine suprachiasmatic nucleus exhibit a circadian rhythm in network coherence in vivo

The suprachiasmatic nucleus (SCN) is composed of functionally distinct subpopulations of GABAergic neurons which form a neural network responsible for synchronizing most physiological and behavioral circadian rhythms in mammals. To date, little is known regarding which aspects of SCN rhythmicity are generated by individual SCN neurons, and which aspects result from neuronal interaction within a network. Here, we utilize in vivo miniaturized microscopy to measure fluorescent GCaMP-reported calcium dynamics in arginine vasopressin (AVP)-expressing neurons in the intact SCN of awake, behaving mice. We report that SCN AVP neurons exhibit periodic, slow calcium waves which we demonstrate, using in vivo electrical recordings, likely reflect burst firing. Further, we observe substantial heterogeneity of function in that AVP neurons exhibit unstable rhythms and relatively weak rhythmicity at the population level. Network analysis reveals that correlated cellular behavior, or coherence, among neuron pairs also exhibited stochastic rhythms with about 33% of pairs rhythmic at any time. Unlike single-cell variables, coherence exhibited a strong rhythm at the population level with time of maximal coherence among AVP neuronal pairs at CT/ZT 6 and 9, coinciding with the timing of maximal neuronal activity for the SCN as a whole. These results demonstrate robust circadian variation in the coordination between stochastically rhythmic neurons and interactions between AVP neurons in the SCN may be more influential than single-cell activity in the regulation of circadian rhythms. Furthermore, they demonstrate that cells in this circuit, like those in many other circuits, exhibit profound heterogenicity of function over time and space.

opencc-by-4.0Dec 2022View details →

Supplementary information files: Gene co-expression network and differential expression analyses of subcutaneous white adipose tissue reveal novel insights into the pathological mechanisms underlying ketosis in dairy cows

Supplementary information files: Gene co-expression network and differential expression analyses of subcutaneous white adipose tissue reveal novel insights into the pathological mechanisms underlying ketosis in dairy cows

opencc-zeroFeb 2023View details →

Gene expression and ELISA data

Obstructive sleep apnea is increasing worldwide, leading to disordered sleep patterns and inflammatory responses in brain and peripheral tissues that predispose individuals to chronic disease. Pro-inflammatory cytokines activate the inflammatory response and their increased expression is observed among mice exposed to experimental sleep fragmentation. Additionally, glucocorticoids are often secreted from the adrenal cortices during sleep loss and are well known to regulate inflammation. However, the temporal dynamics of inflammatory responses and hypothalamic-pituitary-adrenal (HPA) axis activation in relation to acute sleep fragmentation (ASF; 1-24h) are unknown. Male C57BL/6J mice were exposed to ASF or control conditions (no ASF) over specified time intervals (1, 2, 6, and 24 h) to elucidate the timing of onset of glucocorticoid release and pro-inflammatory responses. Cytokine gene expression (IL-1b, TNF-a) in brain and peripheral tissues and serum glucocorticoid and interleukin-6 (IL-6) concentration were measured to determine the temporal relationships of neuroendocrine-immune responses to acute SF. The HPA axis was rapidly activated, leading to elevated serum corticosterone from 1-24 h of ASF compared with controls. This activation was followed by elevated serum IL-6 concentration from 2–24 h of ASF. The tissue to first exhibit increased pro-inflammatory gene expression from ASF was the heart (1 h of ASF). In contrast, pro-inflammatory gene expression was suppressed in the hypothalamus after 1 h of ASF, but elevated after 6 h. Because the HPA axis was elevated throughout ASF, this suggests that brain, but not peripheral, pro-inflammatory responses were rapidly inhibited by glucocorticoid immunosuppression. Instead, activation of the sympathetic nervous system (SNS) may potentiate inflammation in the short-term for peripheral tissues, but further empirical studies are needed. Understanding the mechanisms underlying the onset of inflammatory responses to sleep fragmentation could provide new therapeutic options to individuals coping with sleep disorders.

opencc-by-4.0Feb 2023View details →

Characterization of Continuous Experimentation in Software Engineering: Expressions, Models and Strategies

Systematic Mapping Study's Dataset

opencc-by-4.0Dec 2022View details →

Single-cell RNA sequencing of Sox17-expressing lineages reveals distinct gene regulatory networks and dynamic developmental trajectories

Two seurat objects contains single-cell RNA sequencing data that captures Sox17-expressing lineages during embryogenesis. sox17_integrated_Figure2B.rds : This is a seurat object that contains single-cell RNA sequencing data from integration of GFP+ cells produced from Sox17GFPCre allele marking cells that currently express Sox17 or short-term progeny of Sox17-expressing progenitors and TdTomato+ cells produced from R26LSL.TdTomato reporter allele in the presence of Sox17GFPCre marking long-term progeny of Sox17-expressing progenitors. Inferred cell types in this seurat object reflects Figure 2B in the article. sox17_Prox1_endoderm_Figure5A.rds : This is a seurat object that contain single-cell RNA sequencing data from integration of Sox17- and Prox1-expressing endoderm dataset. Prox-1 expressing endoderm data is from the Willnow et al. Nature(2021). Inferred cell types in this seurat object reflects Figure 5A in the article.

opencc-by-4.0Mar 2023View details →

Data to run analyses present in the paper: Cell specificity of human regulatory annotations and their genetic effects on gene expression

Data for the manuscript: Varshney A., H. VanRenterghem, P. Orchard, A. P. Boyle, M. L. Stitzel, et al., 2019 Cell Specificity of Human Regulatory Annotations and Their Genetic Effects on Gene Expression. Genetics 211: 549–562. <a href="https://doi.org/10.1534/genetics.118.301525">https://doi.org/10.1534/genetics.118.301525</a> The code to generate these data are at GitHub:  https://github.com/ParkerLab/regulatoryAnnotations_comparisons Also see processed data available in this previous Zenodo record: https://zenodo.org/record/1413623

opencc-zeroMar 2023View details →

Association of Wolbachia with gene expression in Drosophila testes

<div> Wolbachia is a genus of intracellular symbiotic bacteria that are widely distributed in arthropods and nematodes. These maternally inherited bacteria regulate host reproductive systems in various ways to facilitate their vertical transmission. Since the identification of Wolbachia in many insects, the relationship between Wolbachia and the host has attracted great interest. Numerous studies have indicated that Wolbachia modifies a variety of biological processes in the host. Previous studies in Drosophila melanogaster (D. melanogaster) have demonstrated that Wolbachia can affect spermatid differentiation, chromosome deposition, and sperm activity in the early stages of spermatogenesis, leading to sperm dysfunction. Here, we explored the putative effect of Wolbachia in sperm maturation using transcriptomic approaches to compare gene expression in Wolbachia-infected and Wolbachia-free D. melanogaster adult testes. Our findings show that Wolbachia affects many biological processes in D. melanogaster adult testes, and most of the differentially expressed genes involved in carbohydrate metabolism, lysosomal degradation, proteolysis, lipid metabolism, and immune response were upregulated in the presence of Wolbachia. In contrast, some genes that are putatively associated with cutin and wax biosynthesis and peroxisome pathways were downregulated. We did not find any differentially expressed genes that are predicted to be related to spermatogenesis in the datasets. This work provides additional information for understanding the Wolbachia-host intracellular relationships.</div>

Modifying the expression of cysteine protease gene PCP affects pollen develop-ment, germination and plant drought tolerance in maize

Figure S1: The sequencing results of pollen grains of T2 mutants. Figure S2: The relative expression levels of PCP were analyzed via RT-qPCR in pcp mutant lines. Data represent means ± SD of three replicates. Significant differences were indicated with different letters (P < 0.05, one-way ANOVA). Figure S3: Pictures of pollen germination and growth in vitro between wild type and transgenic lines after 4 h and 6 h incubation. Scale bar: 100 μm; Figure S4: Phenotypic observation of wild-type and transgenic maize at flowering stage. Scale bar: 10 cm. Figure S5. DAB staining detection of ROS in WT, KO and OE plants under drought stress. Table S1: PCR primers used in this study.

EGID Express R Data File

Date file for EGID Epress

Double shrinking (DOSH), a regression-based algorithm for gene regulatory network inference from co-expression data

Data for the preprint "Double shrinking (DOSH), a regression-based algorithm for gene regulatory network inference from co-expression data". The preprint is live on ResearchSquare: <a href="http://t.researchsquare.com/track/click/31114617/doi.org?p=eyJzIjoiWVJQQUYtT09mMXFoWnRoMGk0SlpQZTZqWWpJIiwidiI6MSwicCI6IntcInVcIjozMTExNDYxNyxcInZcIjoxLFwidXJsXCI6XCJodHRwczpcXFwvXFxcL2RvaS5vcmdcXFwvMTAuMjEyMDNcXFwvcnMuMy5ycy0yNzM4NjgzXFxcL3YxXCIsXCJpZFwiOlwiZDMzODNjZGNhNWNiNGE2Yjk5NWRkY2UyNmIyODI5NTlcIixcInVybF9pZHNcIjpbXCIzZGQwZTAxMmExMzk4NDhkNTAzYjI4ZTBiZmU1Y2QxMDcxNzhlZTgwXCJdfSJ9">10.21203/rs.3.rs-2738683/v1</a>.

opencc-by-4.0Dec 2022View details →

Gene expression of CD4+ T cells in the liver of SIV-infected macaques.

Analysis of RNA transcripts of CD4+ T cells from the liver of healthy (n=3) and SIV infected (n=3) 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.

opencc-by-4.0Feb 2022View details →

Assessing Tumor-Infiltrating Lymphocytes in Breast Cancer: A Proposal for Combining Immunohistochemistry and Gene Expression Analysis to Refine Scoring

Whole tissue scans of histochemistry (H&E) and immunohistochemistry (CD3, CD4, CD8 andCD45) images that have been used to calculate TIL scores. All stainings are numbers for each patient..

Dataset for "Population-level transposable element expression dynamics influence trait evolution in a fungal crop pathogen"

Supplementary Tables Supplementary Table S1: SRA accession list of RNAseq reads. Supplementary Table S2: Genomic localization of TEs in gene elements and 10 kb windows upstream and downstream of the transcription start site (TSS) in the reference genome IPO323. Supplementary Table S3: Genome-wide TE insertion polymorphism (TIPs) in the pathogen population. 0 represents TE absence and 1 represents TE presence. Supplementary Table S4: Gene expression (log-transformed RPKM) values across the population. Supplementary Table S5: Locus-specific transcript abundance at individual TE loci (FPKM) across individuals. Supplementary Table S6: Percent of expressed copies within each TE family in the reference genome IPO323 and percent expressed TE copies in each TE family across the population. Supplementary Table S7: Linkage disequilibrium of TIP in the genome and neighboring SNPs within the 600bp distance from the TE loci. Supplementary Table S8: Genome-wide association mapping of the virulence-associated trait (PLACP: percent leaf area covered by pycnidia) and TE insertion polymorphisms in the genome. Supplementary Table S9: TIPs in the genome significantly associated with metabolite peak intensity variation in the pathogen population (filtered by Bonferroni threshold).

The relationship between the clinical course of SARS-CoV-2 infection with ACE2 and TMPRSS2 expression and polymorphisms

Background The viral S protein and host ACE2 and TMPRSS2 genetic variations may act as a barrier to viral infection or determine susceptibility to COVID-19 infection. Objectives We investigated the relationship between the expression patterns and polymorphisms of the ACE2 and TMPRSS2 receptor genes associated with COVID-19 and the clinical course of COVID-19 infection. Material and methods We studied 147 COVID-19 patients (41 asymptomatic, 53 symptomatic and 53 treated in intensive care unit (ICU) cases) and 33 healthy controls. ACE2 and TMPRSS2 expressions were determined using the One-Run RT Q-PCR kit. Genotypic distributions of Single Nucleotide Polymorphisms (SNP) of ACE2 and TMPRSS2 were obtained by RT-PCR. Results The expressions of ACE2 and TMPRSS2 were different between SARS-CoV-2 positive and negative groups. ACE2 rs714205GG genotype and G-allele showed significant differences in the SARS-CoV-2 positive asymptomatic group. A significant correlation was found between TMPRSS2 rs8134378GA, rs2070788GA, rs7364083GA and rs9974589AC genotypes and SARS-CoV-2 positivity. The rs1978124 C-allele and rs8134378 A-allele were significant in the SARS-CoV-2 positive symptomatic group. TMPRSS2 rs2070788GA was different in all patient groups from the control group. There was a difference between SARS-CoV-2 positive and negative groups for the CTTA haplotype formed by ACE2 variants. The AGCAG and AGAAG haplotypes formed by TMPRSS2 variants were more common in the asymptomatic patient group than in other patient groups. Conclusions Identifying the relationship between host genetic variants and COVID-19 susceptibility will contribute to further studies that will enable new vaccines and potential therapeutic approaches to be applicable.

opencc-by-4.0May 2023View details →

Dataset for Variation in nominal possessive expressions in Danish and Swedish

Dataset for Variation in nominal possessive expressions in Danish and Swedish Alicja Piotrowska https://orcid.org/0000-0002-9868-2964 Adam Mickiewicz University, Poznań, Poland Al. Niepodległości 4, 61-874 Poznań alicja.piotrowska@amu.edu.pl

opencc-by-4.0May 2023View details →

FunMap input expression data matrices

This gzipped tar file contains mRNA and protein expression matrices for 11 different cancer types. Five of them contain both tumor and normal samples, while six of them contain only tumor samples.

opencc-zeroMay 2023View details →

Data for: Divergence of alternative sugar preferences through modulation of the expression and activity of the Gal3 sensor in yeast

Optimized nutrient utilization is crucial for the progression of microorganisms in competing communities. Here we investigate how different budding yeast species and ecological isolates have established divergent preferences for two alternative sugar substrates: Glucose, which is fermented preferentially by yeast, and galactose, which is alternatively used upon induction of the relevant GAL metabolic genes. We quantified the dose-dependent induction of the GAL1 gene encoding the central galactokinase enzyme, and found that a very large diversification exists between different yeast ecotypes and species. The sensitivity of GAL1 induction correlates with the growth performance of the respective yeasts with the alternative sugar. We further define some of the mechanisms, which have established different glucose/galactose consumption strategies in representative yeast strains by modulating the activity of the Gal3 inducer. (1) Optimal galactose consumers, such as Saccharomyces uvarum, contain a hyperactive GAL3 promoter, sustaining highly sensitive GAL1 expression, which is not further improved upon repetitive galactose encounters. (2) Desensitized galactose consumers, such as S. cerevisiae Y12, contain a less sensitive Gal3 sensor, causing a shift of the galactose response towards higher sugar concentrations even in galactose experienced cells. (3) Galactose insensitive sugar consumers, such as S. cerevisiae DBVPG6044, contain an interrupted GAL3 gene, causing extremely reluctant galactose consumption, which however still is improved upon repeated galactose availability. In summary, different yeast strains and natural isolates have evolved galactose utilization strategies, which cover the whole range of possible sensitivities by modulating the expression and/or activity of the inducible galactose sensor Gal3.

opencc-by-4.0Feb 2023View details →

Germline Immunomodulatory Expression Quantitative Trait Loci (ieQTLs) Associated with Immune-Related Toxicity from Checkpoint Inhibition

Robert Ferguson1,2,3*, Vylyny Chat1,2,3*, Leah Morales1,2,3, Danny Simpson1,2,3, Kelsey Monson1,2,3, Elisheva Cohen1,2,3,Sarah Zusin1,2,3, Gabriele Madonna4, Mariaelena Capone4, Ester Simeone4, Anna Pavlick5, Jason Luke6,7, Thomas F Gajewski8,9,10, Iman Osman1,3,11,12, Paolo Antonio Ascierto4, Jeffrey Weber1,3,11, Tomas Kirchhoff1,2,3 1Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA 2Departments of Population Health and Environmental Medicine, New York University- Grossman School of Medicine, New York, NY, USA 3The Interdisciplinary Melanoma Cooperative Group, New York University-Grossman School of Medicine, New York, NY, USA 4Melanoma Cancer Immunotherapy and Innovative Therapy Unit, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Napoli, Italy 5Division of Hematology & Medical Oncology, the Cutaneous Oncology Program, Weill Cornell Medicine and New York-Presbyterian, New York, USA 6Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15213, USA. 7UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA. 8Department of Pathology, University of Chicago, Chicago, IL, USA. 9Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA. 10Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA. 11Department of Medicine, New York University-Grossman School of Medicine, New York, NY, USA 12Ronald O. Perelman Department of Dermatology, New York University-Grossman School of Medicine, New York, NY, USA *These authors contributed equally to the work Corresponding author: Tomas Kirchhoff, PhD ABSTRACT Background: Immune-checkpoint inhibition (ICI) has improved clinical outcomes for metastatic melanoma patients, however, 65-80% of patients treated with ICI experience immune-related adverse events (irAEs). Given the plausible link of irAEs with underlying host immunity, we explored if germline genetic variants controlling the expression of 42 immunomodulatory genes were associated with the risk of irAEs in melanoma patients treated with the single-agent anti- CTLA-4 antibody ipilimumab (IPI). Methods: We identified 42 immunomodulatory expression quantitative trait loci (ieQTLs) most significantly associated with the expression of 382 immune-related genes. These germline variants were genotyped in IPI-treated melanoma patients, collected as part of a multiinstitutional collaboration. We tested the association of ieQTLs with irAEs in a discovery cohort of 95 patients followed by validation in an additional 97 patients. Results: We found that the alternate allele of rs7036417, a variant linked to increased expression of SYK, was strongly associated with an increased risk of grade 3-4 toxicity (OR= 7.46; 95% CI=2.65-21.03; p=1.43E-04). This variant was not associated with response (OR= 0.90; 95% CI=0.37-2.21; p=0.82). Conclusion: We report that rs7036417 associates with increased risk of severe irAEs, independent of IPI efficacy. SYK plays an important role in B-cell/T-cell expansion and increased pSYK has been reported in patients with autoimmune disease. The association between rs7036417 and IPI irAEs in our data suggests a role of SYK over-expression in irAE development. These findings support the hypothesis that inherited variation in immune-related pathways modulate ICI toxicity and suggest SYK as a possible future target for therapies to reduce irAEs.   Keywords: irAEs; germline variants; immune checkpoint inhibition; melanoma Funding: This research was funded by the Italian Ministry of Health (IT-MOH) through “Ricerca Corrente”, grants number M2/2 and L2-1.

opencc-zeroMay 2023View details →

Periodically disturbing biofilms reduces expression of quorum sensing regulated virulence factors in Pseudomonas aeruginosa

The opportunistic pathogen Pseudomonas aeruginosa uses quorum sensing to control the expression of multiple virulence factors. In this dataset, we provide raw data demonstrating that periodically disturbing biofilms composed of P. aeruginosa using a physical force reduces the expression of multiple quorum sensing regulated virulence factors from the three major regulons. This dataset also contains cell density measurements of bacteria both the in biofilm and planktonic state under a variety of conditions that use physical force to manipulate the spatial positioning of bacteria. Finally, the data set contains raw outputs from a network logic model that described the core quorum sensing network. This data is affiliated with the manuscript entitled "Periodically disturbing biofilms reduces expression of quorum sensing regulated virulence factors in Pseudomonas aeruginosa."