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21,320 results for “Transcription”
TAGET: A toolkit for analyzing full-length transcripts from long-read sequencing
<p>Polished transcripts of COLO829 from the PacBio platform. The original web link: https://downloads-ap.pacbcloud.com/public/dataset/Melanoma2019_IsoSeq/PolishedMappedTranscripts/before-SQANTI2filter/.</p>
Aracena et al- Epigenetic variation impacts individual differences in the transcriptional response to influenza infection
<p>-Inputs for Github code</p><p>-Full methylation results</p><p>-Full QTL results</p>
Molecular dynamics trajectories, GROMACS input files, and analysis code from "Rational optimization of a transcription factor activation domain inhibitor" by Basu et. al, Nature Structural & Molecular Biology, 2023
<p>Molecular dynamics trajectories, GROMACS input files, and analysis code from "Rational optimization of a transcription factor activation domain inhibitor" by Basu et. al, Nature Structural & Molecular Biology, 2023</p> <p> </p> <p> </p>
Transcription start sites from capped small RNA-seq of rat nucleus accubmens and prefrontal cortex
<p>Small RNAs of ∼15–60 nt were size selected by denaturing gel electrophoresis starting from total RNA extracted from 14 rat brain tissue dissections. For csRNA libraries, cap selection was followed by decapping, adapter ligation, and sequencing. For input libraries, 10% of small RNA input was used for decapping, adapter ligation, and sequencing. After library quality check by gel electrophoresis, the samples were sequenced using the Illumina NextSeq 500 platform using 75 cycles single end. Sequencing reads were aligned to the rat mRatBN7.2 genome assembly using STAR v2.5.3a aligner with default parameters. Transcriptional start regions were defined using HOMER’s findPeaks tool. </p> <p>Duttke, S.H., Montilla-Perez, P., Chang, M.W., Li, H., Chen, H., Carrette, L.L.G., de Guglielmo, G., George, O., Palmer, A.A., Benner, C., et al. (2022). Glucocorticoid Receptor-Regulated Enhancers Play a Central Role in the Gene Regulatory Networks Underlying Drug Addiction. Front. Neurosci. 16, 858427.</p>
Xrp1 ChIP-seq database (data from Xrp1 is a transcription factor required for cell competition-driven elimination of loser cells)
<p>Xrp1 ChIP-seq data from Baillon et al. 2018, "Xrp1 is a transcription factor required for cell competition-driven elimination of loser cells".</p>
Transcriptional changes in macaques exposed to Sudan virus and treated with a vehicle controls or obeldesivir for 5 or 10 days
<p><span>Normalized Nanostring transcriptomic data (fold2-change- and Benjamini–Hochberg adjusted p-values) were exported as an .xlsx file. Groups include vehicle control (N=3), treated fatal (N=2), and treated survivor subjects administered ODV for 5 (N=3) or 10 days (N=5) compared against a pre-challenge baseline (0 DPI) at each collection timepoint. Any differentially expressed transcripts with a Benjamini-Hochberg false discovery rate (FDR) corrected p-value less than 0.05 were deemed significant. ODV, obeldesivir; DPI, days post infection.</span></p>
LsRTDv1: A reference transcript dataset for accurate transcript-specific expression analysis in lettuce
<p>Accurate quantification of gene and transcript-specific expression, with the underlying knowledge of precise transcript isoforms, is crucial to understanding many biological processes. Analysis of RNA sequencing data has benefited from the development of alignment-free algorithms which enhance the precision and speed of expression analysis. However, such algorithms require a reference transcriptome. Here we present a reference transcript dataset (LsRTDv1) for lettuce, combining long- and short-read sequencing with publicly available transcriptome annotations, and filtering to keep only transcripts with high-confidence splice junctions and transcriptional start and end sites. LsRTDv1 is a valuable resource for the investigation of transcriptional and alternative splicing regulation in lettuce.</p>
An activity-specificity trade-off encoded in human transcription factors
<p>Data repository for the publication <strong>"An activity-specificity trade-off encoded in human transcription factors"</strong>. </p> <p>Imaging datasets with larger sizes can be downloaded here: https://owww.molgen.mpg.de/~TFsuboptimization/</p>
Cell-type-specific mRNA transcription and degradation kinetics in zebrafish embryogenesis from metabolically labeled scRNAseq
<p><span>During embryonic development, pluripotent cells assume specialized identities by adopting particular gene expression profiles. However, systematically dissecting the relative contributions of mRNA transcription and degradation to shaping those profiles remains challenging, especially within embryos with diverse cellular identities.<span> Here, we </span>combine<span> </span>single-cell RNA-Seq and metabolic labeling to capture temporal cellular transcriptomes of zebrafish embryos where newly-transcribed (zygotic) and pre-existing (maternal) mRNA can be distinguished. We then introduce kinetic models to quantify mRNA transcription and degradation rates within individual cell types during their specification. These models reveal highly varied regulatory rates across thousands of genes, coordinated transcription and destruction rates for many transcripts, and link differences in degradation to specific sequence elements. They also identify cell-type-specific differences in degradation, namely selective retention of maternal transcripts within primordial germ cells and enveloping layer cells, two of the earliest specified cell-types. Our study provides a quantitative approach to study mRNA regulation during</span> a dynamic spatio-temporal response<span>.</span></p> <p> </p> <p>This repository contains the raw microscopy data that is analyzed in Figures 6F-I and Supplementary Figure S4 B-D.</p>
Fig1. Gel electrophoresis 2 in Promising use of Polymerase Chain Reaction Associated to Reverse Transcription for the Detection ofthe America-1 Lineage of Canine Distemper Virus
Fig1. Gel electrophoresis 2% agarose
Fig2. Gel electrophoresis Agarose 2 in Promising use of Polymerase Chain Reaction Associated to Reverse Transcription for the Detection ofthe America-1 Lineage of Canine Distemper Virus
Fig2. Gel electrophoresis Agarose 2%.
STORM Data: Transcriptionally active chromatin loops contain both 'active' and 'inactive' histone modifications that exhibit exclusivity at the level of nucleosome clusters
<p>The dataset underlying the SMLM STORM super-resolution images of 'Transcriptionally active chromatin loops contain both ‘active’ and ‘inactive’ histone modifications that exhibit exclusivity at the level of nucleosome clusters'. See Biorxiv paper for details on sample preparation: <a href="https://www.biorxiv.org/content/10.1101/2023.09.03.555774v1.full.pdf">https://www.biorxiv.org/content/10.1101/2023.09.03.555774v1.full.pdf</a>, Pyranose Oxidase STORM buffer on Elyra 7 Zeiss Microscope, processed with Zen Black. Samples are named according to which figures they occur in the above paper.</p>
Data from: Gastrointestinal gd T cells reveal upregulated T-cell transcripts and signaling pathways during peanut oral immunotherapy
<p>Oral immunotherapy (OIT) has been successful in desensitizing patients to offending food allergens, although identification of tissue-resident T cell subsets and cognate pathways leading to desensitization has been challenging. The T cells are a major T-cell subset of mucosal intraepithelial lymphocytes (IELs) and play a significant role in tissue homeostasis and repair. Studies in mouse models suggested a regulatory role of gd T cells in food allergy (FA). Also, peripheral gd T cells from patients analyzed over 24 weeks of peanut OIT were shown to undergo dynamic changes in expression profiles, implicating pathways involved in immune homeostasis. To our knowledge, the role of gd T cells in the intestinal mucosa of FA patients during immunotherapy has not been examined. To this end, we investigated whether gd T cells in the gastrointestinal (GI) tract are modulated during peanut OIT. We hypothesized that GI-resident gd T cells in FA patients would increase during the course of peanut OIT and reveal transcripts and pathways relevant to the mechanisms of peanut desensitization.</p>
Data from: Foraging-induced craniofacial plasticity is associated with an early, robust, and dynamic transcriptional response
<p>Phenotypic plasticity is the ability of a single genotype to vary its phenotype in response to the environment. Plasticity of the skeletal system in response to mechanical input is widely studied, but the timing of its transcriptional regulation is not well-understood. Here we used the cichlid feeding apparatus to examine the transcriptional dynamics of skeletal plasticity over time. Using three closely related species that vary in their ability to remodel bone and a panel of 11 genes, including well studied skeletal differentiation markers and newly characterized environmentally sensitive genes, we examined plasticity at 1, 2, 4 and 8 weeks following the onset of alternate foraging challenges. We found that the plastic species exhibited environment-specific bursts in gene expression at 1 week, followed by a sharp decline in levels, while the species with more limited plasticity exhibited consistently low levels of gene expression. This trend held across nearly all genes, suggesting that it is a hallmark of the larger plasticity regulatory network. We conclude that plasticity of the cichlid feeding apparatus is not the result of slowly accumulating gene expression difference over time, but rather is stimulated by early bursts of environment-specific gene expression followed by a return to homeostatic levels.</p>
Data for: A novel and ubiquitous miRNA-involved regulatory module ensures precise phosphorylation of RNA polymerase II and proper transcription
<p>Proper transcription orchestrated by RNA polymerase II (RNPII) is crucial for cellular development, which relies on the phosphorylation state of RNPII's carboxyl-terminal domain (CTD). Sporangia, developed from mycelia, are essential for the destructive oomycetes<em> Phytophthora</em>, remarkable transcriptional changes are observed during the morphological transition. However, how these changes are rapidly triggered and their relationship with the versatile RNPII-CTD phosphorylation remain enigmatic. Herein, we found that <em>Phytophthora</em> <em>capsici</em> had undergone an elevation of Ser5-phosphorylation in its uncanonical heptapeptide repeats of RNPII-CTD during sporangia development, which subsequently changed the chromosomal occupation of RNPII and primarily activated transcription of certain genes. A cyclin-dependent kinase,<em> </em>PcCDK7, was highly induced and phosphorylated RNPII-CTD during this morphological transition. Mechanistically, a novel DCL1-dependent microRNA, pcamiR1, was found to be a feedback modulator for the precise phosphorylation of RNPII-CTD by complexing with PcAGO1 and regulating the accumulation of PcCDK7. Moreover, this study revealed that the pcamiR1-CDK7-RNPII regulatory module is evolutionarily conserved and the impairment of the balance between pcamiR1 and <em>PcCDK7 </em>could efficiently reduce the growth and virulence of<em> P. capsici</em>. Collectively, this study uncovers a novel and evolutionarily conserved mechanism of transcription regulation that could facilitate correct development and identifies pcamiR1 as a promising target for disease control.</p>
Interview wedding photographer, Napoli, Transcript (AIWP_04_IT_150323)
<p>Wedding photographer Napoli</p> <p>1970</p> <p>since he was 13 works in the busniness of wedding photography</p>
Data from: Pharmacological HIF-1 activation upregulates extracellular vesicle production synergistically with adiponectin through transcriptional induction and protein stabilization of T-cadherin
<p>Pharmacological activation of hypoxia-inducible factor 1alpha (HIF-1α), a hypoxia-responsive transcription factor, has attracted increasing attention due to its efficacy not only in renal anemia but also in various disease models. Our study demonstrated that a HIF-1 activator enhanced exosome production from cultured endothelial cells synergistically with adiponectin, an adipocyte-derived factor, through both transcriptional induction and posttranscriptional stabilization of an adiponectin binding partner, T-cadherin. Increased exosome levels were observed in wild-type mice but not in T-cadherin null mice after consecutive administration of roxadustat. Adiponectin- and T-cadherin-dependent increased exosome production may be involved in the pleiotropic effects of HIF-1 activators.</p>
Monosaccharide transporter OsMST6 is activated by transcription factor OsERF120 to enhance chilling tolerance in rice seedlings
<p>Chilling stress caused by extreme weather is threatening global rice (<em>Oryza sativa</em> L.) production. Identifying components of the signal transduction pathways underlying chilling tolerance in rice would advance molecular breeding. Here, we report that <em>OsMST6</em>, which<em> </em>encodes<em> </em>a monosaccharide transporter, positively regulates the chilling tolerance of rice seedlings. The <em>mst6</em> mutants showed hypersensitivity to chilling, while the <em>OsMST6</em> overexpression lines were tolerant. During chilling stress, OsMST6 transported more glucose into cells to modulate sugar and ABA signal pathways. We showed that the transcription factor OsERF120 could bind to the DRE/CRT element of the <em>OsMST6</em> promoter and activate the expression of <em>OsMST6</em> to positively regulate chilling tolerance. Genetically, OsERF120 was functionally dependent on OsMST6 when promoting chilling tolerance. In summary, OsERF120 and OsMST6 form a new downstream chilling regulatory pathway in rice in response to chilling stress, providing valuable findings for molecular breeding aimed at achieving global food security.</p> <p><span>The stored data is the analysis results of transcriptome data from ZH11 and <em>mst6-1</em> after 0 hours and 4 hours of chilling treatment. These data form the basis for the transcriptome data visualization in the article.</span></p>
Identification and expression analysis of transcription factors in the Carallia brachiata genome
<p>Rhizophoraceae has 2 terrestrial genera and 4 marine genera. The intertidal zone in which marine mangroves are located is known for its low oxygen and high salinity. Marine and terrestrial genera have evolved distinct adaptive characteristics, among which viviparous reproduction is the most unique. To investigate the genetic foundations difference underlying the adaptive mechanisms of marine–terrestrial genera, we selected two species from Rhizophoraceae. <em>Kandelia obovata</em> is marine and viviparous, and <em>Carallia brachiata</em> is terrestrial and non-viviparous.<em> </em>We compared their transcriptome of 8 tissues (root, stem, leaf, flower, ovule, fruit, seed, embryo) and found that the mature reproductive organs (fruit, seed, embryo) of <em>K. obovata </em>did not reduce metabolic activity compared to <em>C. brachiata</em>. The reproductive organs of <em>K. obovata</em> were regulated by the same gene set as vegetative organs. This contrasted with <em>C. brachiata</em>. Eight kinds of hormone transduction genes were up-regulated in the seed of <em>K. obovata</em>. Finally, and most importantly, the transcriptional factors AP2 and ARF families were significantly more expressed in the reproductive organs of <em>K. obovata</em> than in those of <em>C. brachiata</em>. At the same time, the ERF family was more expressed in its roots. The findings suggested that the hormone transduction may contribute to viviparous initiation. Transcriptional factors were quite crucial for mangroves' adaptation to wetlands.</p>
Promptuarium genealogicum by Carl Keller-Escher: Transcription Full Texts and Image File Links
<div> <div>This dataset contains image links, full texts, and metadata of the seven volumes of the *Promptuarium genealogicum* by Carl Keller-Escher (1851–1916). This genealogical work, spanning approximately 2,800 pages, provides information on members of 258 historical Zurich families, some dating back to the 16th century.</div> </div>
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