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2,420 results for “differential gene expression”
Figure 2 in Differential gene expression pattern and plasma sex steroids during testicular development in Genyatremus luteus (Perciforme: Haemulidae) (Bloch, 1790)
Figure 2. Steroid concentrations in the blood plasma of male Genyatremus luteus individuals during their reproductive cycle. (A) 11-ketotestosterone. (B) 17 α-hidroxy progesterone. (C) 17β-estradiol. Data are represented as mean ± SEM. abc: indicates statistically significant difference (p<0.05).
Pelagomonas calceolata gene expression levels in different nitrogen conditions and differential expression analysis.
<p>These files contains the expression levels and DESeq2 results of <em>Pelagomonas calceolata</em> genes cultivated with different nitrate conditions. Two strains of <em>P. calceolata </em>(RCC100 and RCC697) were cultivated and their RNAs reads were aligned on the predicted genes of <em>P. calceolata</em> RCC100 genome: <a href="https://www.ncbi.nlm.nih.gov/Traces/wgs/CAKKNE01?display=download" rel="nofollow">https://www.ncbi.nlm.nih.gov/Traces/wgs/CAKKNE01?display=download</a></p> <p>The following culture conditions were analysed :</p> <p>882 µM of Nitrate (RCC100 and RCC697) </p> <p>441 µM of Nitrate (RCC100)</p> <p>220 µM of Nitrate (RCC100 and RCC697)</p> <p>50 µM of Nitrate (RCC697)</p> <p>882 µM Cyanate (RCC100)</p> <p>882 µM Ammonia (RCC100)</p> <p>441 µM Urea (RCC100)</p> <p><a href="../api/records/12582059/draft/files/20230427_RCC100-Nitrate_transcriptomes_rawcounts.tsv/content" target="_blank" rel="noopener noreferrer">20230427_RCC100-Nitrate_transcriptomes_rawcounts.tsv</a> : the file contains the raw read counts of RCC100 in 6 culture conditions in triplicate + the gene names = 19 columns.</p> <p><a href="../api/records/12582059/draft/files/20230427_RCC100-Nitrate_transcriptomes_TPM.tsv/content" target="_blank" rel="noopener noreferrer">20230427_RCC100-Nitrate_transcriptomes_TPM.tsv</a> : same data normalized in transcript per kb per million mapped reads (TPM).</p> <p><a href="../api/records/12582059/draft/files/20230427_RCC100-Nitrate_transcriptomes_rawcounts.tsv/content" target="_blank" rel="noopener noreferrer">20230427_RCC697-Nitrate_transcriptomes_rawcounts.tsv</a> : the file contains the raw read counts of RCC697 of 3 culture conditions in triplicate + the gene names = 10 columns.</p> <p><a href="../api/records/12582059/draft/files/20230427_RCC100-Nitrate_transcriptomes_TPM.tsv/content" target="_blank" rel="noopener noreferrer">20230427_RCC697-Nitrate_transcriptomes_TPM.tsv</a> : same data normalized in transcript per kb per million mapped reads (TPM).</p> <p><span>Differential expression analysis (DESeq2) was performed by pairwise comparisons between the standard condition (882 µM nitrate) and low-nitrate conditions (50, 220 or 441 µM nitrate) or changing nitrogen sources (882 µM ammonium, 882 µM cyanate and 441 µM urea). Each DESeq-results_RCCxxx_xxx.tsv file contains 6 columns : <em>P.calceolata </em>gene name, base Mean, log2 Fold Change, standard error value (lfcSE), pvalue and adjusted pvalue (padj).<br></span></p>
Human-specific tandem repeat expansion and differential gene expression during primate evolution
<p>THIS DATASET IS PART OF THE FOLLOWING STUDY:<br> <a href="https://www.pnas.org/content/early/2019/10/22/1912175116">https://www.pnas.org/content/early/2019/10/22/1912175116</a></p> <p> </p> <p>THE RAW SEQUENCING 10x GENOMICS READS CAN BE DOWNLOADED FROM SRA:<br> <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA593056">https://www.ncbi.nlm.nih.gov/bioproject/PRJNA593056</a></p> <p><br> ORIGINAL UPLOAD: 09/06/2019</p> <p>UPDATES: 10/28/2019; 01/27/2020</p> <p>DESCRIPTION: Contigs were assembled using Phased-SV (<a href="https://www.nature.com/articles/s41467-018-08148-z">Chaisson et al, Nature Communications 2019</a>) on six human haplotypes (i.e., H0 and H1 in NA19240, HG00514, and HG00733), and six nonhuman haplotypes (this study, H0 and H1 in Clint the chimpanzee, Kamilah the gorilla, and Susie the orangutan). The long read data (PacBio CLR) from NHPs were phased into haplotypes H0 and H1 using linked reads from 10X Genomics prior to assembly, whenever possible. If not possible (e.g., in the case of long runs of homozygosity regions), long reads from both haplotypes were used to generate a "squished assembly". Using human haplotype data, we identified 21,442 polymorphic STRs/VNTRs, followed by a targetted phasing of these regions in the three NHPs. All of the human and nonhuman primate contigs were padded by 2 kbp both upstream and downstream, followed by mapping against the human reference (GRCh38). We did the same for "squished assemblies" from a Yoruban individual, CHM13, and three NHPs as described in <a href="https://science.sciencemag.org/content/360/6393/eaar6343">Kronenberg et al, Science 2018</a>. The BAM and BAI files in this dataset contain the alignment of all these contigs against GRCh38.</p>
Fig. 1. Differentially expressed genes between infected and uninfected P in Subtle transcriptomic response of Eurasian perch (Perca fluviatilis) associated with Triaenophorus nodulosus plerocercoid infection
Fig. 1. Differentially expressed genes between infected and uninfected P. fluviatilis in a) spleen and b) liver tissues. Filled-in and empty boxes on the top of each plot represent infected and uninfected individuals, respectively. N/A indicates unknown protein.
Práctica de transcriptómica: expresión diferencial de genes aplicado a la producción de alimentos / Practical Transcriptomics: Differential gene expression applied to food production
<p>Data for the eLearning tutorial Practical Transcriptomics: Differential gene expression applied to food production</p> <p>Datos para el tutorial eLearning Práctica de transcriptómica: expresión diferencial de genes aplicado a la producción de alimentos</p>
RNA-seq data of "Transcriptome analyses of leaves reveal that hexanoic acid priming differentially regulate gene expression in contrasting Coffea arabica cultivars"
<p>This dataset represent FASTQ gziped files from the study "Transcriptome analyses of leaves reveal that hexanoic acid priming differentially regulate gene expression in contrasting <em>Coffea arabica</em> cultivars" (<a href="https://doi.org/10.3389/fsufs.2021.735893">https://doi.org/10.3389/fsufs.2021.735893</a>). Sequencing was done using an Illumina Novaseq 6000 instrument, paired-sequencing (2 X150 bp). Sample details are also available at https://www.ebi.ac.uk/ena/browser/view/ERA6282544.</p> <p> </p> <p>All filenames have the following naming scheme:</p> <p>LCS7609_DS_AAA_leafBBB_(R1 or R2).fq.gz</p> <p>AAA stands for the abbreviations:</p> <p>- CC (Coffea arabica cv Catuai control)</p> <p>- CHx (Coffea arabica cv Catuai exposed to Hexanoic acid)</p> <p>- OC (Coffea arabica cv Obatã control)</p> <p>- OHx (Coffea arabica cv Obatã exposed to Hexanoic acid)</p> <p>BBB stands for the number of biological replicate (1, 2 or 3).</p> <p> </p> <p> </p> <p> </p>
Results of the differential gene expression analysis in SIV infection in Chlorocebus sabaeus and Macaca mulatta
<p>Results of differential gene expression analysis in SIV infection in Chlorocebus sabaeus and Macaca mulatta.</p> <p>From the transcriptome data repository MACE (http://mace.ihes.fr)</p>
Differentially-expressed genes in blood in response to lipopolysaccharide in three rodent species
<p>Infection tolerance in rodents was examined by injecting single-dose lipopolysaccharide (LPS) to induce inflammation in <span><em>Peromyscus</em> <em>leucopus</em></span><span> (LL stock), the white-footed deermouse also reservoir for Lyme disease and </span><span><em>Mus</em> <em>musculus</em></span><span> (outbred CD-1 breed), the house mouse, and </span><span><em>Rattus</em> <em>norvegicus</em></span><span>, the brown rat (Fischer strain). Reaction to LPS was analyzed in the blood of challenged rodents and compared to control animals. As natural reservoirs of zoonoses deermice show significant anti-inflammatory response as described in "An Infection-Tolerant Mammalian Reservoir for Several Zoonotic Agents Broadly Counters the Inflammatory Effects of Endotoxin" (</span><a href="https://doi.org/10.1128/mBio.00588-21)" rel="noopener"><span>https://doi.org/10.1128/mBio.00588-21)</span></a><span>. The project and the description of the samples are described under the following NCBI BioProjects: PRJNA975149 (</span><a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA975149" rel="noopener"><span>https://www.ncbi.nlm.nih.gov/bioproject/PRJNA975149)</span></a><span> for mouse and deermouse and PRJNA973677 (</span><a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA973677)" rel="noopener"><span>https://www.ncbi.nlm.nih.gov/bioproject/PRJNA973677)</span></a><span>. This project is a follow-up project focusing on the transcriptomic analysis of the whole blood bulk RNA-seq and further analysis of differentially expressed genes (DEG) between the treatment arm and controls. Complete fold change and false discovery rate for all three rodent species used for the current Dryad set are previously published (<a href="https://doi.org/10.7280/D1470Z">https://doi.org/10.7280/D1470Z</a>). Here we report that deermice tolerance to infection is partly due to lower expression of interferon-gamma in comparison to mice and rats. <br></span></p>
R code for differential gene expression and enrichment analyses
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Raw differential gene expression data, data S1, from: Molecular cascades and cell type-specific signatures in ASD revealed by single cell genomics
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Data from: Differential gene expression in relation to mating system in Peromyscine rodents
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Data from: Depletion of lamins B1 and B2 promotes chromatin mobility and induces differential gene expression by a mesoscale-motion dependent mechanism
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Differentially-expressed genes in blood in response to lipopolysaccharide in three rodent species
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Co-exposure of uranyl acetate and sodium arsenite differentially alters gene expression in CD3/CD28 activated CD4+ T-cells.
Communities in the western region of the United States experience environmental exposure to metal mixtures from living in proximity to numerous unremediated abandoned uranium mines. Metals including arsenic and uranium co-occur in and around these sites at levels higher than the United States Environmental Protection Agency maximum contaminant levels. To address the potential effect of these metals on the activation of CD4+ T-cells, we used RNA sequencing methods to determine the effect of exposure to uranyl acetate, sodium arsenite or a mixture of uranyl acetate and sodium arsenite. Oxidative stress is a mechanism proposed for metal toxicity, but findings for uranium differ across cell models. No significant changes in oxidative stress genes were detected for uranyl acetate, in contrast to sodium arsenite. Sodium arsenite induced a dose dependent effect on activation associated gene expression, targeting immune response genes at the lower dose. While uranyl acetate alone did not significantly alter activation associated gene expression, the mixture demonstrated a combined effect relative to sodium arsenite alone. The results demonstrate the need to investigate uranium alone and in metalloid mixtures at environmentally relevant concentrations to better understand the toxicological impact of these mixtures on T-cell activation, function and immune dysregulation.
Data from: Seasonally sympatric but allochronic: differential expression of hypothalamic genes in a songbird during gonadal development
Allochrony, the mismatch of reproductive schedules, is one mechanism that can mediate sympatric speciation and diversification. In songbirds, the transition into breeding condition and gonadal growth is regulated by the hypothalamic-pituitary-gonadal (HPG) axis at multiple levels. We investigated whether the difference in reproductive timing between two, seasonally sympatric subspecies of dark-eyed juncos (Junco hyemalis) was related to gene expression along the HPG axis. During the sympatric pre-breeding stage, we measured hypothalamic and testicular mRNA expression of candidate genes via qPCR in captive male juncos. For hypothalamic mRNA, we found our earlier breeding subspecies had increased expression of gonadotropin-releasing hormone (GnRH) and decreased expression of androgen receptor, estrogen receptor alpha, and mineralocorticoid receptor (MR). Subspecies did not differ in expression of hypothalamic gonadotropin-inhibitory hormone (GnIH) and glucocorticoid receptor (GR). While our earlier breeding subspecies had higher mRNA expression of testicular GR, subspecies did not differ in testicular luteinizing hormone receptor, follicle-stimulating hormone receptor, or MR mRNA expression levels. Our findings indicate increased GnRH production and decreased hypothalamic sensitivity to sex steroid negative feedback as factors promoting differences in the timing of gonadal recrudescence between recently diverged populations. Differential gene expression along the HPG axis may facilitate species diversification under seasonal sympatry.
Data from: Sperm competitive advantage of a rare mitochondrial haplogroup linked to differential expression of mitochondrial oxidative phosphorylation genes
Maternal inheritance of mitochondria creates a sex-specific selective sieve through which mitochondrial mutations harmful to males but not females accumulate and contribute to sexual differences in longevity and disease susceptibility. Because eggs and sperm are under disruptive selection, sperm are predicted to be particularly vulnerable to the genetic load generated by maternal inheritance, yet evidence for mitochondrial involvement in male fertility is limited and controversial. Here, we exploit the coexistence of two divergent mitochondrial haplogroups (A and B2) in a Neotropical arachnid to investigate the role of mitochondria in sperm competition. DNA profiling demonstrated that B2-carrying males sired more than three times as many offspring in sperm competition experiments than A males, and this B2 competitive advantage cannot be explained by female mitochondrial haplogroup or male nuclear genetic background. RNA-Seq of testicular tissues implicates differential expression of mitochondrial oxidative phosphorylation (OXPHOS) genes in the B2 competitive advantage, including a 22-fold upregulation of <i>atp8</i> in B2 males. Previous comparative genomic analyses have revealed functionally significant amino acid substitutions in differentially expressed genes, indicating that the mitochondrial haplogroups differ not only in expression but also in DNA sequence and protein functioning. However, mitochondrial haplogroup had no effect on sperm number or sperm viability, and, when females were mated to a single male, neither male haplogroup, female haplogroup nor the interaction between male/female haplogroup significantly affected female reproductive success. Our findings therefore suggest that mitochondrial effects on male reproduction may often go undetected in noncompetitive contexts and may prove more important in nature than is currently appreciated.
Differentially expressed genes in berries and rachis of berry shrivel grape clusters used to prepare figures for a review
<p>Grapevine berry shrivel is a ripening disorder leading to significant economic losses in the worldwide wine and table grape industries. Sugar accumulation stops early after ripening onset accompanied with cell death in berreis and subtending pecicels and rachis finally resulting in berry shrinkage. To date, the triggers of BS remain unknown. The dataset supports figures prepared for an review which aims to summarize and critically discuss the current knowledge. Data are expressed as differentially expressed genes obtained from grape berries samples collected at six developmental stages (pre- until post-veraison) analysed with RNASeq and two pooled samples (pre- and BS symptomatic) from the rachis analyzed with a microarray study. Extracted information focus on primary metabolic processes including sugar transport and metabolism, organic acid metabolism, stress signaling and cell as well as cell wall organisation. Data are mean values of three biological represent and presented as log2 fold changes including statistical information. A meta-data sheet provides the most relevant information and references. </p>
Methylation and gene expression data from: Differential DNA methylation across environments has no effect on gene expression in the eastern oyster
<p>1. It has been hypothesized that environmentally induced changes to gene body methylation could facilitate adaptive transgenerational responses to changing environments.</p> <p>2. We compared patterns of global gene expression (Tag-seq) and gene body methylation (reduced representation bisulfite sequencing) in 80 eastern oysters (<i>Crassostrea virginica</i>) from six full-sib families, common gardened for 14 months at two sites in the northern Gulf of Mexico that differed in mean salinity.</p> <p>3. At the time of sampling, oysters from the two sites differed in mass by 60% and in parasite loads by nearly two orders of magnitude. They also differentially expressed 35% of measured transcripts. However, we observed differential methylation at only 1.4% of potentially methylated loci in comparisons between individuals from these different environments, and little correspondence between differential methylation and differential gene expression.</p> <p>4. Instead, methylation patterns were largely driven by genetic differences among families, with a PERMANOVA analysis indicating nearly a two orders of magnitude greater number of genes differentially methylated between families than between environments.</p> <p>5. An analysis of CpG observed/expected values (CpG O/E ) across the <i>C. virginica</i> genome showed a distinct bimodal distribution, with genes from the first cluster showing the lower CpG O/E values, greater methylation, and higher, and more stable gene expression, while genes from the second cluster showed lower methylation, and lower and more variable gene expression.</p> <p>6. Taken together, the differential methylation results suggest that only a small portion of the <i>C. virginica</i> genome is affected by environmentally induced changes in methylation. At this point, there is little evidence to suggest that environmentally induced methylation states would play a leading role in regulating gene expression responses to new environments.</p>
Single cell multiomic analysis identifies key genes differentially expressed in innate lymphoid cells from COVID-19 patients
<p>Innate lymphoid cells (ILCs) are enriched at mucosal surfaces where they respond rapidly to environmental stimuli and contribute to both tissue inflammation and healing. To gain insight into the role of ILCs in the pathology and recovery from COVID-19 infection, we employed a multi-omic approach consisting of Abseq and targeted mRNA sequencing to respectively probe the surface marker expression, transcriptional profile and heterogeneity of ILCs in peripheral blood of patients with COVID-19 compared with healthy controls. We found that the frequency of ILC1 and ILC2 cells was significantly increased in COVID-19 patients. Moreover, all ILC subsets displayed a significantly higher frequency of CD69-expressing cells, indicating a heightened state of activation. ILC2s from COVID-19 patients had the highest number of significantly differentially expressed (DE) genes. The most notable genes DE in COVID-19 vs healthy participants included a) genes associated with responses to virus infections and b) genes that support ILC self-proliferation, activation and homeostasis. In addition, differential gene regulatory network analysis revealed ILC-specific regulons and their interactions driving the differential gene expression in each ILC. Overall, this study provides mechanistic insights into the characteristics of ILC subsets activated during COVID-19 infection.</p>
Table with results of differential gene expression analysis in the controlled environment for fin tissues.
<p>Differences between transcriptomes of three Cottus fish lineages were assessed under controlled, laboratory conditions. Two tissues were investigated: fins and livers. Present table shows results of the differential gene expression analysis performed on fin tissues of Cottus fish. Base-mean, Log-2-fold change. standard error, statistics and associated p-values and FDR-corrected p-values are given for every contrast possible in our experimental design.</p>
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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.