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54,099 results for “Expression”
CollecTRI Data for Investigation of SETBP1 gene expression and transcription factor activity across human tissues
<p>Here we provide the human CollecTRI prior (accessed May 2023) for inference of TF activity across 31 GTEx tissues using multivariate linear modeling method decoupleR.<br> <br> The `human_prior_tri.csv` includes 1,178 unique TFs (referred to as the source) that target 6,627 unique genes (referred to as targets) to give us 42,595 interactions in the CollecTRI prior input. Interactions are represented as a + or - 1 (mor).</p>
Simultaneous estimation of gene regulatory network structure and RNA kinetics from single cell gene expression
<p>Supplemental Data 1 is single-cell response to rapamycin count data first sequenced in this work and deposited in GEO with accession GSE242556. It is a 173348 rows × 5847 columns TSV.GZ file where the first row is a header, the first 5843 columns are integer gene counts, and the final 4 columns ('Gene', 'Replicate', 'Pool', and 'Experiment') are cell-specific metadata.</p> <p>Supplemental Data 2 is bulk response to rapamycin count data first sequenced in this work. It is a 33 rows × 5847 columns TSV.GZ file where the first row is a header, the first 5843 columns are integer gene counts, and the final 4 columns ('Oligo', 'Time', 'Replicate', and 'Sample_barcode') are sample-specific metadata.</p> <p>Supplemental Data 3 is single-cell count data published as GSE125162 and re-analyzed with the pipeline used for single-cell quantification in this work. It is a 65068 rows × 5850 columns TSV.GZ file where the first row is a header, the first 5843 columns are integer gene counts, and the final 7 columns ('Condition', 'Sample', 'Genotype_Group', 'Genotype_Individual', 'Genotype', 'Replicate', 'Cell_Barcode') are cell-specific metadata.</p> <p>Supplemental Data 4 is the four deep learning models trained in this work. It is a TAR.GZ file containing the final biophysical transcription/decay model, the pre-trained decay model, the velocity prediction model, and the count prediction model. Each model file is an h5 file containing a pytorch model that can be loaded with supirfactor\_dynamical.read().</p> <p>Supplemental Data 5 is the prior knowledge network used to constrain the models for TF interpretability. It is a 1574 rows × 204 columns [Genes x TFs] TSV.GZ file where the first row is a header with TF names, the first column is an index of gene names, and TF-gene interactions are indicated by non-zero values in the matrix. There are 2799 TF-gene interactions.</p> <p><br> Supplemental Table 6 is the oligonucleotide sequences used in this work. It is a TSV file with a header row.</p> <p>Supplemental Table 7 is the yeast strains used in this work. It is a TSV file with a header row.</p> <p>Supplemental Table 8 is gene metadata used in this work (e.g. Ribosomal Protein gene labels, etc). It is a TSV file with a header row.</p> <p>Supplemental Table 9 is FY4/5 growth curve data generated in this work. It is a 20 rows × 7 columns TSV file where the first row is a header with replicate IDs, the first column is an index of times in minutes, and values are cell densities in YPD culture, in units of 10$^6$ cells / mL.</p> <p>Supplemental Data 10 is a TAR.GZ file containing the yeast SacCer3 genome, modified to add UTR sequences, that was used to generate transcripts for kallisto pseudoalignment in this work.</p>
Leaf litter, soil, and periphyton gene expression along freshwater to marine gradients in Everglades National Park (FCE LTER), Florida, USA, January 2021 and April 2021
We collected leaf litter, periphyton, and soil along freshwater to marine gradients at SRS-2, SRS-4, SRS-6, TS/PH-2, TS/Ph-3, TS/Ph-7a, and TS/Ph-10. Samples were collected in January and April of 2021 to understand how microbial communities respond to and influence the breakdown of organic matter along freshwater to marine transects. Data collection for this project is complete. For each site and litter pair we collected a subset of 2-3 g wet mass of litter, a grab sample of soil, and a grab sample of periphyton for each site. All subsamples were preserved at -20°C until extraction, which took place up to a year after initial collection. Samples were sent to Novogene (Novogene Co. Ltd., Beijing, China) for the total RNA extraction followed by metatranscriptome sequencing. We selected n = 12 genes/gene families encoding for focal enzymes to investigate which are important to the breakdown of organic matter: Dioxygenases (associated with aerobic respiration), Sulfatases (associated with the release of sulfates from complex molecules), sulfite reductases (associated with sulfite reduction), methyl coenzyme M reductase and formylmethanofuran (associated with methanogenesis), nitrite reductases (associated with nitrite reduction), cellobiosidase, glucosidase, and xylosidase (associated with cellulose breakdown), phenol oxidase (associated with lignin breakdown), acid phosphatase (associated with phosphate acquisition in acidic environments), and alkaline phosphatase (associated with phosphate acquisition in basic environments). For each gene/family of interest, we searched all annotated transcripts for all entries corresponding to that gene/family and combined all values for a total expression. We selected n = 6 monophyletic microbial functional groups, representing sulfate reducers, sulfate oxidizers, methane oxidizers, methanogens, nitrite oxidizers, and ammonia oxidizers associated with sulfate and methane cycling. We filtered all annotated transcripts for all specie
Spatial integration of transcription and splicing in a dedicated compartment sustains monogenic antigen expression in African trypanosomes
<p>This repository contains the data for the manuscript <a href="https://doi.org/10.1038/s41564-020-00833-4">https://doi.org/10.1038/s41564-020-00833-4</a>.</p> <p>The HiC analysis pipeline can be found at <a href="https://github.com/bgbrink/PRJEB35632">https://github.com/bgbrink/PRJEB35632</a>.</p> <p><strong>Abstract</strong></p> <p>Highly selective gene expression is a key requirement for antigenic variation in several pathogens, allowing evasion of host immune responses and maintenance of persistent infections. African trypanosomes — parasites that cause lethal diseases in humans and livestock — employ an antigenic variation mechanism that involves monogenic antigen expression from a pool of >2,600 antigen-coding genes. In other eukaryotes, the expression of individual genes can be enhanced by mechanisms involving the juxtaposition of otherwise distal chromosomal loci in the three-dimensional nuclear space. However, trypanosomes lack classical enhancer sequences or regulated transcription initiation. In this context, it has remained unclear how genome architecture contributes to monogenic transcription elongation and transcript processing. Here, we show that the single expressed antigen-coding gene displays a specific inter-chromosomal interaction with a major messenger RNA splicing locus. Chromosome conformation capture (Hi-C) revealed a dynamic reconfiguration of this inter-chromosomal interaction upon activation of another antigen. Super-resolution microscopy showed the interaction to be heritable and splicing dependent. We found a specific association of the two genomic loci with the antigen exclusion complex, whereby VSG exclusion 1 (VEX1) occupied the splicing locus and VEX2 occupied the antigen-coding locus. Following VEX2 depletion, loss of monogenic antigen expres- sion was accompanied by increased interactions between previously silent antigen genes and the splicing locus. Our results reveal a mechanism to ensure monogenic expression, where antigen transcription and messenger RNA splicing occur in a specific nuclear compartment. These findings suggest a new means of post-transcriptional gene regulation.</p>
PsPM-trSP4: SCR measurement in response to face photographs withangry, neutral, and fearful expression while subjected to auditory distractors
<p>This dataset includes skin conductance response (SCR) measurements for each of 42 healthy unmedicated participants (21 males and 21 females aged 25.2 +/- 4.0 years) in response to 38 face photographs (modified from the Karolinska Directed Emotional Faces set, KDEF), each presented once with angry, neutral, and fearful expression for 1 s each. Meanwhile, participants were listening to regular or random distractor sounds, as described in Bach et al. (2015). ITI was selected randomly on each trial from 7.5 s, 9.0 s, or 10.5 s (misprinted in the publications), plus a variable delay of around 0.1 s for image loading. The experiment was preceded by a 2-minute resting period and divided into 3 blocks, separated by resting periods. Each resting period begins and ends with an event marker in the SCR recordings.</p>
Dataset related to article "NKp46-expressing human gut-resident intraepithelial Vδ1 T cell subpopulation exhibits high antitumor activity against colorectal cancer"
<p>γδ T cells account for a large fraction of human intestinal intraepithelial lymphocytes (IELs) endowed with potent antitumor activities. However, little is known about their origin, phenotype, and clinical relevance in colorectal cancer (CRC). To determine γδ IEL gut specificity, homing, and functions, γδ T cells were purified from human healthy blood, lymph nodes, liver, skin, and intestine, either disease-free, affected by CRC, or generated from thymic precursors. The constitutive expression of NKp46 specifically identifies a subset of cytotoxic Vδ1 T cells representing the largest fraction of gut-resident IELs. The ontogeny and gut-tropism of NKp46+/Vδ1 IELs depends both on distinctive features of Vδ1 thymic precursors and gut-environmental factors. Either the constitutive presence of NKp46 on tissue-resident Vδ1 intestinal IELs or its induced expression on IL-2/IL-15-activated Vδ1 thymocytes are associated with antitumor functions. Higher frequencies of NKp46+/Vδ1 IELs in tumor-free specimens from CRC patients correlate with a lower risk of developing metastatic III/IV disease stages. Additionally, our in vitro settings reproducing CRC tumor microenvironment inhibited the expansion of NKp46+/Vδ1 cells from activated thymic precursors. These results parallel the very low frequencies of NKp46+/Vδ1 IELs able to infiltrate CRC, thus providing insights to either follow-up cancer progression or to develop adoptive cellular therapies.</p> <p> </p> <p>This dataset is created with fcs files form, in order to guarantee the access we attach a pdf information about</p>
[Dataset] Spatial and temporal variability of the 365-nm albedo of Venus observed by the camera on board Venus Express
<p>This is the derived data, presented in a publication entitled "Spatial and temporal variability of the 365-nm albedo of Venus observed by the camera on board Venus Express" (JGR:Planet, doi: 10.1029/2019JE006271). See the paper for details. See 'Readme.txt' for the file descriptions.</p>
DS7_LH_ Lodola et al_Sci Adv_2019_Gene expression Studies
<p>RT-PCR on ECFCs seeded on P3HT and subjected to Light stimulation. </p>
Data and supplementary material in support of article "Can robots express facial emotions dominantly enough for use in dementia care?"
<p>Data and supplementary material in support of article "Vlachos, E. and Tan, Z. H. (2020). Can robots express facial emotions dominantly enough for use in dementia care?, <em>International Psychogeriatrics</em>, Cambridge University Press". </p> <p>Our objective is to evaluate the recognition, and denomination of the six basic emotional facial expressions as displayed by a social robot to persons with dementia, and to compare it with the results from the evaluation of static photographs of humans from the Paul Ekman database in order to investigate the differences in recognition rates among the two stimuli.</p>
Extensive qPCR analysis reveals altered gene expression in middle ear mucosa from cholesteatoma patients
<p><strong>Abstract</strong></p> <p>The middle ear is a small and hard to reach compartment, limiting the amount of tissue that can be extracted and the possibilities for studying the molecular mechanisms behind diseases like cholesteatoma. In this paper 14 reference gene candidates were evaluated in the middle ear mucosa of cholesteatoma patients and two different control tissues. <em>ACTB</em> and <em>GAPDH</em> were shown to be the optimal genes for the normalisation of target gene expression when investigating middle ear mucosa in multiplex qPCR analysis. Validation of reference genes using <em>c-MYC</em> expression confirmed the suitability of <em>ACTB</em> and <em>GAPDH</em> as reference genes and showed an upregulation of <em>c-MYC</em> in middle ear mucosa during cholesteatoma. The occurrence of participants of the innate immunity, <em>TLR2</em> and <em>TLR4</em>, were analysed in order to compare healthy middle ear mucosa to cholesteatoma. Analysis of <em>TLR2</em> and <em>TLR4</em> showed variable results depending on control tissue used, highlighting the importance of selecting relevant control tissue when investigating causes for disease. It is our belief that a consensus regarding reference genes and control tissue will contribute to the comparability and reproducibility of studies within the field.</p>
Illuminating the impact of diel vertical migration on visual gene expression in deep-sea shrimp
<p>Diel vertical migration (DVM) of marine animals represents one of the largest migrations on our planet. Migrating fauna are subjected to a variety of light fields and environmental conditions that can have notable impacts on sensory mechanisms, including an organism's visual capabilities. Among deep-sea migrators are oplophorid shrimp, that vertically migrate hundreds of meters to feed in shallow waters at night. These species also have bioluminescent light organs that emit light during migrations to aid in camouflage. The organs have recently been shown to contain visual proteins (opsins) and genes that infer light sensitivity. Knowledge regarding the impacts of vertical migratory behavior, and fluctuating environmental conditions, on sensory system evolution is unknown. In this study, the oplophorid <i>Systellaspis debilis</i> was either collected during the day from deep waters or at night from relatively shallow waters to ensure sampling across the vertical distributional range. <i>De novo </i>transcriptomes of light sensitive tissues (eyes/photophores) from the <i>Day/Night </i>specimens were sequenced and analyzed to characterize opsin diversity and visual/light interaction genes. Gene expression analyses were also conducted to quantify expression differences associated with DVM. Our results revealed an expanded opsin repertoire among the shrimp and differential opsin expression that may be linked to spectral tuning during the migratory process. This study sheds light on the sensory systems of a bioluminescent invertebrate and provides additional evidence for extraocular light sensitivity. Our findings further suggest opsin coexpression and subsequent fluctuations in opsin expression may play an important role in diversifying the visual responses of vertical migrators.</p>
Xpresso: Predicting gene expression levels from genomic sequences
<p>Xpresso: Predicting gene expression levels from genomic sequences<br> <br> More info at:<br> Publication: https://doi.org/10.1016/j.celrep.2020.107663<br> Website: https://xpresso.gs.washington.edu/<br> Github: https://github.com/vagarwal87/Xpresso</p>
nNOS-expressing interneurons control basal and behaviorally evoked arterial dilation in somatosensory cortex of mice
<p>Cortical neural activity is coupled to local arterial diameter and blood flow. However, which neurons control the dynamics of cerebral arteries is not well understood. We dissected the cellular mechanisms controlling the basal diameter and evoked dilation in cortical arteries in awake, head-fixed mice. Locomotion drove robust arterial dilation, increases in gamma band power in the local field potential (LFP), and increases calcium signals in pyramidal and neuronal nitric oxide synthase (nNOS)-expressing neurons. Chemogenetic or pharmocological modulation of overall neural activity up or down caused corresponding increases or decreases in basal arterial diameter. Modulation of pyramidal neuron activity alone had little effect on basal or evoked arterial dilation, despite pronounced changes in the LFP. Modulation of the activity of nNOS-expressing neurons drove changes in the basal and evoked arterial diameter without corresponding changes in population neural activity.</p>
mRNA expression data of genes related to mitochondrial quality control in hepatopancreas of the two marine bivalves, Mytilus edulis and Crassostrea gigas, during short-term hypoxia/reoxygenation stress
<p>Coastal environments commonly experience strong oxygen fluctuations. Resulting hypoxia/reoxygenation stress can negatively affect mitochondrial functions, since oxygen deficiency impairs ATP generation, whereas a surge of oxygen causes mitochondrial damage by oxidative stress mechanisms. Marine intertidal bivalves are adapted to fluctuating oxygen conditions, yet the underlying molecular mechanisms that sustain mitochondrial integrity and function during oxygen fluctuations are not yet well understood. We used targeted mRNA expression analysis to determine the potential involvement of the mitochondrial quality control mechanisms in responses to short-term hypoxia (24 h at <0.01% O<sub>2</sub>) and subsequent reoxygenation (1.5 h at 21% O<sub>2</sub>) in two hypoxia-tolerant marine bivalves, the Pacific oysters <em>Crassostrea gigas</em> and the blue mussels <em>Mytilus edulis</em>. To test these hypotheses, We focused on the transcript levels of the following marker genes: for mitochondrial fission and fusion - <em>mfn</em>2 (encoding mitofusin 2), <em>opa</em>1 (mitochondrial dynamin-like 120kDa protein), <em>dnm</em>1<em>l </em>(dynamin-1-like protein), <em>mff</em> (mitochondrial fission factor), <em>fis</em>1 (mitochondrial fission protein 1); for protein and DNA quality control - <em>tsfm</em> (encoding mitochondrial translation elongation factor Ts), <em>lonp</em>1 (mitochondrial Lon protease), <em>spg</em>7 (paraplegin), <em>oma</em>1 (mitochondrial metalloendopeptidase OMA1), <em>clpB</em> (mitochondrial caseinolytic matrix peptidase chaperone subunit B), <em>atp</em>23 (mitochondrial inner membrane protease ATP23), <em>twnk</em> (mitochondrial twinkle mtDNA helicase); and for mitophagy - <em>mieap</em> (encoding mitochondrial eating protein), <em>hyou</em>1 (hypoxia upregulated protein 1), <em>prkn</em> (parkin), <em>pink</em>1 (PTEN- induced kinase 1), and <em>pgam</em>5 (mitochondrial serine/threonine protein phosphatase PGAM5). The revealed species-specific differences in the expression of the mitochondrial quality control pathways shed light on the potentially important mechanisms of mitochondrial protection against H/R-induced damage that might contribute to hypoxia tolerance in marine bivalves. </p>
Data from: Populus euphratica WRKY1 binds the promoter of PeHA1 to enhance gene expression and salt tolerance
<p>Plasma membrane proton pumps play a crucial role in maintaining ionic homeostasis in salt-resistant <i><span>Populus euphratica</span></i> under saline conditions<i><span>. </span></i>High levels of NaCl (200 mM) induced <i><span>PeHA1</span></i> expression in <i><span>P. euphratica</span></i> roots and leaves. We isolated a 2022-bp promoter fragment upstream of the translational start of <i><span>PeHA1 </span></i>from<i><span> P. euphratica</span></i>. The promoter-reporter construct <i><span>PeHA1-pro</span></i>::<i><span>GUS</span></i> was transferred to tobacco plants, demonstrating that β-glucuronidase activities increased in root, leaf, and stem tissues under salt stress. DNA affinity purification sequencing revealed that PeWRKY1 protein targeted the<i><span> PeHA1</span></i> gene. We assessed the salt-induced transcriptional response of PeWRKY1 and its interaction with <i><span>PeHA1</span></i> in <i><span>P. euphratica</span></i>. PeWRKY1 binding to the <i><span>PeHA1 </span></i>W-box in promoter region was verified by a yeast one-hybrid assay, electrophoretic mobility shift assay, luciferase reporter assay, and virus-induced gene silencing. Transgenic tobacco plants overexpressing <i><span>PeWRKY1</span></i> had improved expression of <i><span>NtHA4, </span></i>which has a cis-acting W-box in the regulatory region, and H<sup><span>+</span></sup> pumping activity in both in vivo and in vitro assays. We conclude that salt stress upregulated <i><span>PeHA1</span></i> transcription due to the binding of PeWRKY1 to the W-box in the promoter region of <i><span>Pe</span></i><i><span>HA1</span></i>. Thus, we conclude that enhanced H<sup><span>+</span></sup> pumping activity enabled salt-stressed plants to retain Na<sup><span>+</span></sup> homeostasis.</p>
ACE2 EXPRESSION LEVELS IN THE BRAIN AND EYE
<p>To Whom It May Concern:</p> <p>As evidenced by multiple research studies, the SARS-CoV2 virus employs the angiotensin converting enzyme 2 (ACE 2) cell surface receptor to gain entry into host cells; this is a necessary first step for SARS-CoV2 invasion, replication and multiplication within human host cells; </p> <p>To ascertain what types of cells and tissues might be the most susceptible to SARS-CoV2 invasion, we have quantified ACE2 expression (at the mRNA level and some at the protein level) in about ~100 different cell types and tissues of the human brain, eye and central nervous system (CNS);</p> <p>Some of the data appear in this recent report from our laboratory:</p> <p>Lukiw WJ, Pogue A, Hill JM. SARS-CoV-2 Infectivity and Neurological Targets in the Brain. Cell Mol Neurobiol. 2020 Aug 25:1–8. doi: 10.1007/s10571-020-00947-7. Epub ahead of print. PMID: 32840758; PMCID: PMC7445393.</p> <p>and in the figures and tables associated with this publication; [appended; please also refer to the Abstract below]</p> <p>Another very recent report has been submitted to the Journal Cellular and Molecular Neurobiology (15 November 2020) for peer-review and is tentatively entitled:</p> <p><em><strong>‘ACE2 receptor expression in the human visual system” </strong></em></p> <p>These data should be of sincere interest to SARS-CoV2 and COVID-19 researchers and expand our understanding of potential cell and tissue targets bearing the ACE2 receptor for SARS-CoV2 invasion and infectivity, and suggest possible visual and neurological routes for SARS-CoV2-cellular entry during the COVID-19 pandemic.</p> <p>Yours truly,</p> <p>Walter J. Lukiw BS, MS, PhD, Professor of Neuroscience and Ophthalmology, Bollinger Professor of Alzheimer’s disease, LSU Neuroscience Center and Department of Ophthalmology, Louisiana State University Health Sciences Center, 2020 Gravier Street, Room 904, New Orleans LA 70112 USA </p> <p>TEL (504) 599-0842; EMAIL wlukiw@lsuhsc.edu </p> <p>================================================================================</p> <p>Paper of interest:</p> <p><strong>Lukiw WJ, Pogue A, Hill JM. SARS-CoV-2 Infectivity and Neurological Targets in the Brain. Cell Mol Neurobiol. 2020 Aug 25:1–8. doi: 10.1007/s10571-020-00947-7. Epub ahead of print. PMID: 32840758; PMCID: PMC7445393.</strong></p> <p><strong>Abstract</strong></p> <p>The gateway for invasion by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into human host cells is via the angiotensin-converting enzyme 2 (ACE2) transmembrane receptor expressed in multiple immune and nonimmune cell types. SARS-CoV-2, that causes coronavirus disease 2019 (COVID-19; CoV-19) has the unusual capacity to attack many different types of human host cells simultaneously via novel clathrin- and caveolae-independent endocytic pathways, becoming injurious to diverse cells, tissues and organ systems and exploiting any immune weakness in the host. The elicitation of this multipronged attack explains in part the severity and extensive variety of signs and symptoms observed in CoV-19 patients. To further our understanding of the mechanism and pathways of SARS-CoV-2 infection and susceptibility of specific cell- and tissue-types and organ systems to SARS-CoV-2 attack in this communication we analyzed ACE2 expression in 85 human tissues including 21 different brain regions, 7 fetal tissues and 8 controls. Besides strong ACE2 expression in respiratory, digestive, renal-excretory and reproductive cells, high ACE2 expression was also found in the amygdala, cerebral cortex and brainstem. The highest ACE2 expression level was found in the pons and medulla oblongata in the human brainstem, containing the medullary respiratory centers of the brain, and may in part explain the susceptibility of many CoV-19 patients to severe respiratory distress.</p> <p><strong>Keywords: </strong>Alzheimer’s disease; Angiotensin-converting enzyme 2 (ACE2) receptor; COVID-19; CoV-19; Coronavirus; Hartnup's disease; SARS-CoV-2; miRNA-5197; microRNA; single stranded RNA (ssRNA).</p> <p> </p> <p>================================================================================</p>
Predicting placenta transcriptional regulatory interactions based on spatial gene expression data and convolutional neural network
<p><strong>Aims:</strong> The dysfunction of placenta development is correlated to the defects of pregnancy and fetal growth. The detailed molecular mechanism of placenta development is not identified in human due to the lack of material in vivo. Image-based reconstructions of GRN are still very underdeveloped.</p> <p><strong>Methods and Results:</strong> In this study, first-trimester chorionic villus and decidua tissues were collected. Next, we present a machine-learning system to infer gene interaction networks of the human placenta from immunofluorescence images of trophoblast specific transcription factors obtained by a high-resolution scanner.</p> <p><strong>Conclusions:</strong> The experimental results show that deep learning models reveal regulatory roles that have not yet been fully recognized. The spatial expression data reveal new regulatory relationships that traditional experiments have failed to recognize, and has allowed the development of gene regulation networks based on the spatial distribution of gene expression. We demonstrate the effectiveness of this approach in building networks using high-resolution images of the human placenta. Our analysis is of certain significance for further exploration of the development of the placenta and the occurrence of pregnancy-related diseases in the future. The datasets and analysis provide a useful source for the researchers in the field of the maternal-fetal interface and the establishment of pregnancy.</p>
Electron density and altitude of the main ionospheric peak of Mars as observed by Mars Express instruments. Archived data for the paper "Seasonal and geographical variability of the Martian ionosphere from Mars Express observations", submitted to JGR-Planets
<p>This repository contains archived data for the manuscript "Seasonal and geographical variability of the Martian ionosphere from Mars Express observations", published in Journal of Geophysical Research-Planets. Details about the methods to generate the data can be found in the paper.</p> <p>5 data files plus 2 readme text files are included.</p> <p>The file MEx_ionpeak.dat (described in the readme file README_ionpeak.txt) contains the peak electron densities and peak altitudes resulting from 34539 observations. Each record includes 14 columns. The content of each column is:</p> <p>Column 1: Instrument providing the observation (MARSIS or MaRS)<br> Column 2: Mars Year at which the observation was obtained (from MY27 to MY33)<br> Column 3: Solar Longitude (Ls) of the observation (unit: degrees)<br> Column 4: Latitude of the observation (unit: degrees)<br> Column 5: Longitude of the observation (unit: degrees)<br> Column 6: Solar Zenith Angle (SZA) of the observation (unit: degrees)<br> Column 7: F10.7 solar proxy index at 1 Astronomic Unit (unit: solar flux units)<br> Column 8: Peak electron density measured by the instrument (unit: cm-3)<br> Column 9: Peak electron density at the subsolar point, i.e., corrected for the SZA variation (unit: cm-3)<br> Column 10: Peak electron density at the subsolar point and at F10.7 (1AU)=100, i.e., corrected for the SZA and the solar radiation output variations (unit: cm-3)<br> Column 11: Peak electron density at the subsolar point, at F10.7 (1AU)=100 and corrected for the seasonal variation (unit: cm-3)<br> Column 12: Peak altitude measured by the instrument (unit: km)<br> Column 13: Peak altitude at the subsolar point, i.e. corrected for the SZA variation (unit: km)<br> Column 14: Peak altitude at the subsolar point and corrected for the seasonal variation (unit: km)</p> <p> </p> <p>The files eprofiles_MaRS.dat, eprofiles_MARSIS_prof1.dat, eprofiles_MARSIS_prof2.dat and eprofiles_MARSIS_prof3.dat contain 4 electron density profiles. They are described in the file README_eprofiles.txt. Each file includes 2 columns, the first one being the altitude (unit: km) and the second one the electron density (unit: cm-3).</p> <p> </p> <p>Contact: Francisco Gonzalez-Galindo, ggalindo@iaa.es<br> </p>
Biogeographic parallels in thermal tolerance and gene expression variation under temperature stress in a widespread bumble bee
<p>Global temperature changes have emphasized the need to understand how species adapt to thermal stress across their ranges. Genetic mechanisms may contribute to variation in thermal tolerance, providing evidence for how organisms adapt to local environments. We determine physiological thermal limits and characterize genome-wide transcriptional changes at these limits in bumble bees using laboratory-reared <em>Bombus vosnesenskii</em> workers. We analyze bees reared from latitudinal (35.7–45.7°N) and altitudinal (7–2154 m) extremes of the species' range to correlate thermal tolerance and gene expression among populations from different climates. We find that critical thermal minima (CT<sub>MIN</sub>) exhibit strong associations with local minimums at the location of queen origin, while critical thermal maximum (CT<sub>MAX</sub>) was invariant among populations. Concordant patterns are apparent in gene expression data, with regional differentiation following cold exposure, and expression shifts invariant among populations under high temperatures. Furthermore, we identify several modules of co-expressed genes that tightly correlate with critical thermal limits and temperature at the region of origin. Our results reveal that local adaptation in thermal limits and gene expression may facilitate cold tolerance across a species range, whereas high temperature responses are likely constrained, both of which may have implications for climate change responses of bumble bees.</p>
FIG. 5 in Gender expression in Sedum praealtum A. DC. (Crassulaceae) in Central Veracruz, Mexico
FIG. 5. — Floral display size in Sedum praealtum A. DC. (Crassulaceae): A, number of inflorescences; B, number of flowers; C, sex ratio (female-phase flowers/ total number of flowers). Values are means ± SE.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.