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25,372 results for “Transcriptomics”
Gecarcinus lateralis - Eyestalk Ganglia Transcriptome
<p><i><strong>Gecarcinus lateralis</strong></i><strong> - Eyestalk Ganglia Transcriptome Assembly</strong></p><p>Assembled <i>de novo</i> using the methods in Pérez-Moreno et al.(2023) with a multi-kmer multi-assembler approach (Trinity + rnaSpades) and processed via the EvidentialGene pipeline.</p><p>Nucleotide and amino acid sequence assemblies in FASTA format.</p><p> </p><p> </p>
What happens when the lights are left on? Transcriptomic and phenotypic habituation to light pollution
<p>Artificial light at night (ALAN) is one of the most ubiquitous human-induced environmental stressors. ALAN can induce immediate behavioral and physiological changes in animals, sometimes leading to severe health consequences. Nevertheless, many organisms persist in light-polluted environments and may have mechanisms of habituating to ALAN, reducing responses to repeated exposure over time. The capacity for animals to habituate to ALAN has yet to be tested experimentally. We conducted a 6-month repeated-measures experiment with zebra finches (<em>Taeniopygia</em> <em>guttata</em>) to test whether birds can habituate to repeated ALAN exposure. We measured individual changes in behavior, physiology (oxidative stress and telomere attrition), and gene expression to test for concordance among behavioral, physiological, and transcriptomic responses to ALAN. We present evidence of tolerance to chronic ALAN exposure, persistent behavioral responses lasting 8 weeks post-exposure, and habituation to subsequent re-exposure. We found no changes in telomere attrition and a decrease in oxidative stress associated with ALAN exposure, indicating potential protective effects of long-term dim ALAN. Changes in blood transcriptome within individuals revealed unique responses to both previous ALAN exposure and subsequent re-exposure. These results represent organismal resilience to chronic stressors and shed light on the capacity of individuals to persist in an increasingly light-polluted world.</p>
Transcriptome data from silica-preserved leaf tissue reveals gene flow patterns in a Caribbean bromeliad
<p>Transcriptome sequencing is a cost-effective approach that allows researchers to study a broad range of questions. However, to preserve RNA for transcriptome sequencing, tissue is often kept under special conditions, such as immediate ultracold freezing. Here, we demonstrate that RNA can be obtained from six-month-old, field-collected samples stored in silica gel at room temperature. Using these transcriptomes, we explore the evolutionary relationships of the genus Pitcairnia (Bromeliaceae) in the Dominican Republic and infer barriers to gene flow.</p>
Similar transcriptomic responses to early and late drought stresses produce divergent phenotypes in sunflower (Helianthus annuus L.)
<p>Cultivated sunflower (<em>Helianthus</em> <em>annuus</em> L.) exhibits numerous phenotypic and transcriptomic responses to drought. However, the ways in which these responses vary with differences in drought timing and severity are insufficiently understood. We used phenotypic and transcriptomic data to evaluate the response of sunflower to drought scenarios of different timing and severity in a common garden experiment. Using a semi-automated outdoor high-throughput phenotyping platform, we grew six oilseed sunflower lines under control and drought conditions. Our results reveal that similar transcriptomic responses can have disparate phenotypic effects when triggered at different developmental time points. Leaf transcriptomic responses, however, share similarities despite timing and severity differences (e.g., 523 differentially expressed genes (DEGs) were shared across all treatments), though increased severity elicits greater differences in expression, particularly during vegetative growth. Across treatments, DEGs were highly enriched for genes related to photosynthesis and plastid maintenance. A co-expression analysis identified a single module (M8) enriched in all drought stress treatments. Genes related to drought, temperature, proline biosynthesis, and other stress responses were overrepresented in this module. In contrast to transcriptomic responses, phenotypic responses were largely divergent between early and late drought. Early-stressed sunflowers responded to drought with reduced overall growth, but became highly water-acquisitive during recovery irrigation, resulting in overcompensation (higher aboveground biomass and leaf area) and a greater overall shift in phenotypic correlations, whereas late-stressed sunflowers were smaller and more water use-efficient. Taken together, these results suggest that drought stress at an earlier growth stage elicits a change in development that enables greater uptake and transpiration of water during recovery, resulting in higher growth rates despite similar initial transcriptomic responses.</p>
Multi-Nucleic Acid Interaction Mapping in Single Cell (MUSIC) for simultanouse chromatin, RNA-chromatin and transcriptome mapping at single cell resolution
<p><a href="https://doi.org/10.1101/2023.06.28.546457">MUSIC manuscript:</a> Joint profiling of multiplex chromatin interactions, gene expression, and RNA-chromatin associations in single cells of the human brain.</p> <p>MUSIC-docker is the customized pipeline to process the raw fastq files to bam files: http://sysbiocomp.ucsd.edu/public/wenxingzhao/MUSIC_docker/intro.html.</p> <p>Each bam file records the final output of our single cell mixed species analysis. Read name recods the cell barcode, complex barcode and I7 index. For each DNA/RNA read, read header contains <code>raw read name</code>| <code>BC3</code>_<code>BC2</code>_<code>BC1</code> - <code>10x barcode</code> # <code>UMI</code>. Details of the read name can be found here: http://sysbiocomp.ucsd.edu/public/wenxingzhao/MUSIC_docker/step.html#demultiplexing.</p> <p>merge_DNA [RNA]_human [mouse].sort.bam: bam file of DNA [RNA] reads from the mix species library (H1+E14) that can uniquely mapped to the human [mouse] genome. PCR duplicates have been removed. </p> <p> </p> <p> </p> <p> </p> <p> </p>
Data from: Transcriptome analysis reveals the mechanism underlying rapid changes in the early phase brain of bi-directional sex change in Trimma okinawae
<p>Teleost fish exhibit remarkable sexual plasticity and display divergent developmental systems including hermaphroditism. One of the more fascinating model systems of sexual plasticity is socially controlled sex change, which is often observed in coral reef fish. The Okinawa rubble goby, <em>Trimma okinawae</em>, is a bi-directional sex change fish that can rapidly change its sex in both directions depending on social circumstances. Although behavioral and neuro-endocrinal sex change occurs within an hour and is believed to trigger gonadal changes, the underlying mechanisms remain poorly understood. In this study, we conducted a de novo transcriptome analysis of the <em>T. okinawae</em> brain and identified genes that were differentially expressed between the sexes and genes that were immediately controlled by social stimulation causing a sex change. We found that a larger number of genes are regulated during the male-to-female transition compared with a change from female to male. Several genes showed concordant expression shifts regardless of the sex change direction. Furthermore, some were associated with histone modification in nerve cells and regulated in the same direction. Overall, we identified genes that regulate the rapid behavioral and neuroendocrinal control of sex change and provide insight into the mechanism of sexual plasticity in teleost fish.</p>
In silico spatial transcriptomic editing at single-cell resolution
<p>The data for training the GAN (Inversion) model and reproduce the results reported in the paper </p>
Systematic evaluation with practical guidelines for single-cell and spatially resolved transcriptomics data simulation under multiple scenarios
<p>All total 152 datasets are collected in the benchmarking study.</p> <p>Every dataset contains two parts: the gene expression matrix (or well-established model by dynwrap for trajectory) and the data information including the data id, repository, accession number, URL, technology platform, species, organ (source), cell number, gene number, data type, ERCC spike-in, dilution factor, volume, group condition, treatment, batch information and cluster labels.</p> <p>There are 23 datasets (data79-data101) for evaluating the simulation ability for cell trajectories which are derived from another Zenodo repository (https://zenodo.org/record/1443566).</p>
Supplemental data for "Transcriptomic Profiling of the Bovine Endosalpinx and Endometrium to Identify Putative Embryokines"
<p>Supplemental data for paper describing expression of genes encoding for cell-signaling ligands in the oviduct and endometrium of cows. </p>
Transcriptomic profiles of MCF7-derived tamoxifen resistant cell lines
<p>We report mRNA profiles of human breast cancer cell lines, MCF7 parental, and MCF7-derived tamoxifen-resistant cell lines MCF7-TR1 and MCF7-TR2.</p> <p>These cells have been previously described in </p> <p>Ines Barone, Lauren Brusco, Guowei Gu, Jennifer Selever, Amanda Beyer, Kyle R. Covington, Anna Tsimelzon, Tao Wang, Susan G. Hilsenbeck, Gary C. Chamness, Sebastiano Andò, and Suzanne A.W. Fuqua. Loss of Rho GDIα and Resistance to Tamoxifen via Effects on Estrogen Receptor α. J Natl Cancer Inst. 2011 Apr 6; 103(7): 538–552. PMID: 21447808</p>
Data for: The relative impact of parental and current environment on plant transcriptomes depends on type of stress and genotype
<p>Through developmental plasticity, an individual organism integrates influences from its immediate environment with those due to the environment of its parents. While both effects on phenotypes are well documented, their relative impact has been little studied in natural systems, especially at the level of gene expression. We examined this issue in four genotypes of the annual plant <em>Persicaria maculosa</em> by varying two key resources light and soil moisture in both generations. Transcriptomic analyses showed that the relative effects of parent and offspring environment on gene expression (i.e., the number of differentially expressed transcripts, DETs) varied both for the two types of resource stress and among genotypes. For light, immediate environment induced more DETs than parental environment for all genotypes (although the precise proportion of parental versus immediate DETs varied among genotypes). By contrast, the relative effect of soil moisture varied dramatically among genotypes, from 8-fold more DETs due to parental than immediate conditions to 10-fold fewer. These findings provide evidence at the transcriptome level that the relative impacts of parental and immediate environment on the developing organism may depend on the environmental factor and vary strongly among genotypes, providing potential for the interplay of these developmental influences to evolve.</p>
Comprehensive Re-annotation and Transcriptome Analysis Provide Insights into Pepper Development and Ascorbic Acid Biosynthesis
<p>This archive contains high-quality gene annotation file termed v2a of the pepper reference genome CA59 and gene expression file in pepper development in the pepper "Comprehensive Re-annotation and Transcriptome Analysis Provide Insights into Pepper Development and Ascorbic Acid Biosynthesis"</p>
ALA induced transcriptome and single cell microscopy of M.tuberculosis
<p> <strong>Single cell microscopy of porphyeins in vegetative and dormant <em>Mycobacterium tuberculosis</em>. Confocal fluorescence microscopy, life-time measurements, and microspectrofluorimetry. </strong>Fluorescence lifetime measurements were performed on a PicoQuant MicroTime 200 confocal scanning system (Pico-Quant GmbH, Berlin, Germany) based on an Olympus IX-71 inverted fluorescence microscope (Japan). SymphoTime® software was used for data collection. Fluorescence spectra were recorded in the confocal mode of the MicroTime 200 system using a Shamrock 163 spectrograph with a Newton DU-970 camera (Andor, UK).</p> <p><strong>Transcriptomic analysis of cells of <em>M. tuberculosis </em>in a vegetative state and under transition into dormant state upon administration of exogenous ALA.</strong> The quality of the resulting libraries was checked using the Fragment Analyzer. Quantitative analysis was performed by qPCR. After quality control and assessment of DNA quantity, the pool of libraries was sequenced on an Illumina NovaSeq 6000 instrument (length of reads - 150 bp on both sides of the fragments). FASTQ files were generated using bcl2fastq v2.20 Conversion Software (Illumina). The quality data string record format is Phred 33. As a result, 1,107,614,502 reads were received. </p> <pre>This study was funded by Russian Science Foundation grant 19-15-00324.</pre>
Data-driven transcriptomics analysis identifies PCSK9 as a novel key regulator in liver aging. (Histology Images)
<p>These are the histology images on "Data-driven transcriptomics analysis identifies PCSK9 as a novel key regulator in liver aging."</p>
Morphological and transcriptomic responses/acclimations of erect-type submerged macrophyte Hydrilla verticillata both at low-light exposure and light recovery phases
<p><span>Light intensity is a determinant for submerged macrophytes. Little is known about their molecular responses to low-light exposure, despite being more informative and responsive than morphological traits. For erect-type submerged macrophytes, the stem is more crucial relative to the leaf in acclimation to low-light stress, but receives less attention. We determined</span> <span>morphological and stem transcriptomic responses/acclimations of <em>Hydrilla verticillata</em> to extremely and mildly low light (7.2 and 36 μmol photons m<sup>–2</sup> s<sup>–1</sup>, respectively), i.e. EL and ML, with the radiation intensity of 180 μmol photons m<sup>–2</sup> s<sup>–1</sup> as the control. Low-light exposure continued for nine days, followed by a seven-day recovery phase (180 μmol photons m<sup>–2</sup> s<sup>–1</sup>). At the exposure phase, the low-light treatments, in particular the EL, decreased relative growth ratio, but induced greater height and longer stem internode distance and epidermal cell. Such responses/acclimations continued into the recovery phase, despite more or less changes in the magnitude. Transcriptome showed that the photosynthetic system was inhibited at the exposure phase, but the macrophyte adjusted hormone synthesis relating to cell division and elongation. Moreover, the EL activated cell stress responses such as DNA repair. Following light recovery, the macrophyte exhibited strong-light response, although energy metabolism enhanced. Especially, the EL-enriched pathways relating to anthocyanin synthesis at such phase, indicating an activation of photoprotective mechanism. Our findings suggest that negative influences of low light occur at both low-light exposure and recovery phases, but submerged macrophytes would acclimate to light environments. Transcriptome can show the molecular basis of plant responses/acclimations, including but not limited to morphology. This study establishes a bridge connecting morphological and molecular responses/acclimations.</span></p>
Data from: Genomic and transcriptomic analyses reveal polygenic architecture for ecologically-important functional traits in aspen (Populus tremuloides Michx.)
<p>Intraspecific genetic variation in foundation species such as aspen (<em>Populus</em> <em>tremuloides</em> Michx.) shapes their impact on forest structure and function. Identifying genes underlying ecologically important traits is key to understanding that impact. Previous studies, using single-locus genome-wide association (GWA) analyses to identify candidate genes, have identified fewer genes than anticipated for highly heritable quantitative traits. Mounting evidence suggests that polygenic control of quantitative traits is largely responsible for this "missing heritability" phenomenon. Our research characterized the genetic architecture of 30 ecologically important traits using a common garden of aspen through genomic and transcriptomic analyses. A multilocus association model revealed that most traits displayed a highly polygenic architecture, with most variation explained by loci with small effects (likely below the detection levels of single-locus GWA methods). Consistent with a polygenic architecture, our single-locus GWA analyses found only 38 significant SNPs in 22 genes across 15 traits. Next, we used differential expression analysis on a subset of aspen genets with divergent concentrations of salicinoid phenolic glycosides (key defense traits). This complementary method to traditional GWA discovered 1,243 differentially expressed genes for a polygenic trait. Soft clustering analysis revealed three gene clusters (241 candidate genes) involved in secondary metabolite biosynthesis and regulation. Our work reveals that ecologically important traits governing higher-order community- and ecosystem-level attributes of a foundation forest tree species have complex underlying genetic structures and will require methods beyond traditional GWA analyses to unravel.</p>
Data from: Transcriptome and exosome proteome analyses provide insights into the mantle exosome involved in nacre color formation of pearl oyster Pinctada fucata martensii
<p>The pearl oyster <em>Pinctada fucata martensii</em> is an economically important species of marine pearl culture, and tissue of mantle plays an essential role in pearl formation. Here, the extracted exosomes from mantle of <em>P. f. martensii</em> were analyzed by quantitative protein TMT sequencing. We wanted to verify if exosomes are the important vehicle in the process of biomineralization (e.g., pearl and shell formation), especially the color formation in shellfish. Finally, we got some results which indicated the importance of exosomes in sides of proteins, and it can also contribute to other researches related to the exosomes or pearl oyster.</p>
Data used in paper "Deciphering driver regulators of cell fate decisions from single-cell transcriptomics data with CEFCON"
<p>This directory contains the data resources of the following paper:</p> <p>"Deciphering driver regulators of cell fate decisions from single-cell transcriptomics data with CEFCON"</p>
Reference transcriptome assembly of a protogynous sex change fish, harlequin sandsmelt (Parapercis pulchella)
<p>Reference transcriptome sequences (superTranscripts) of a marine teleost fish <em>Parapercis pulchella</em>.</p> <p>This dataset is a part of our work, "Reference transcriptome assembly of a protogynous sex change fish, harlequin sandsmelt (<em>Parapercis</em> pulchella)" published in <em>Marine Genomics</em>.</p> <p>https://doi.org/10.1016/j.margen.2024.101086</p> <p> If you use this dataset, plese cite the above paper.</p> <p>Raw RNA-seq data and <em>de novo </em>assembled sequences generated by Trinity have been deposited in NCBI/DDBJ/EMBL under accession PRJDB16534.</p> <p>This dataset is generated from Trinity raw-assembled sequences using superTranscripts method (Corset, Lace). </p> <p>Functional annotations were conducted using eggNog-mapper, KEEG Automatic Annotation Server (KAAS), and reciprocal BLAST best-hit analysis against medaka's protein sequences.</p> <p> </p> <p>The codes for generating these data are deposited in GitHub (<a href="https://github.com/yaoakifumi/Ppul-reference-transcriptome">https://github.com/yaoakifumi/Ppul-reference-transcriptome</a>).</p> <p> </p>
Single-cell and spatially resolved transcriptomic data of mouse regenerative livers under normal and fibrotic conditions
<p>A single-cell spatial-temporal transcriptomic atlas of liver regeneration under normal and fibrotic condition, including a total of 30 mouse liver samples obtained from 15 normal and 15 fibrotic mice at timepoints Day 0, 1, 2, 3, and 7 after a partial hepatectomy (PHx) procedure with three replicates for each time point, followed by the scRNA-seq and SRT sequencing for each sample using the Stereo-seq platform. </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.