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21,320 results for “Transcription”
Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin
<p>We prepared these datasets associated with the paper “Genome-scale imaging of the 3D organization and transcriptional activity of chromatin” published in Cell: <a href="https://doi.org/10.1016/j.cell.2020.07.032">https://doi.org/10.1016/j.cell.2020.07.032</a>.</p> <p>Please find detailed descriptions of individual data files in the README_August 2020.txt.</p> <p>We provide example codes to load and analyze these datasets in: <a href="https://github.com/ZhuangLab/Chromatin_Analysis_2020_cell">https://github.com/ZhuangLab/Chromatin_Analysis_2020_cell</a>.</p> <p>If you use these datasets, please cite our Cell paper.</p>
Transient intracellular acidification regulates the core transcriptional heat shock response
<p>Heat shock induces a conserved transcriptional program regulated by heat shock factor 1 (Hsf1) in eukaryotic cells. Activation of this heat-shock response is triggered by heat-induced misfolding of newly synthesized polypeptides, and so has been thought to depend on ongoing protein synthesis. Here, using the budding yeast <em>Saccharomyces cerevisiae</em>, we report the discovery that Hsf1 can be robustly activated when protein synthesis is inhibited, so long as cells undergo cytosolic acidification. Heat shock has long been known to cause transient intracellular acidification which, for reasons which have remained unclear, is associated with increased stress resistance in eukaryotes. We demonstrate that acidification is required for heat shock response induction in translationally inhibited cells, and specifically affects Hsf1 activation. Physiological heat-triggered acidification also increases population fitness and promotes cell cycle reentry following heat shock. Our results uncover a previously unknown adaptive dimension of the well-studied eukaryotic heat shock response. </p>
Oral Music of the Maghreb and the Mashriq and the digital encoding of scores / transcriptions
<p>2<sup>nd</sup> Lecture</p>
Single-cell repertoire and transcriptome sequencing reveals clonally expanded and transcriptionally distinct lymphocytes in aged CNS
<p>Single-cell repertoire and transcriptome sequencing reveals clonally expanded and transcriptionally distinct lymphocytes in aged CNS. Gene expression and immune receptor repertoire sequencing was performing for both B and T cells. This dataset contains the VDJ sequencing information for the four samples. Each B cell and T cell library was sequenced across four lanes. </p> <p> </p> <p>Files with _WT_ in their name correspond to the young (4-6 week B6 mice) </p> <p>Files with _12_ in their name before the BDJ or VDJ text correspond to the 12-month-old cohort.</p> <p>Files with _18_ in their name before the BDJ or VDJ text correspond to the 18-month-old cohort in which four brains were pooled.</p> <p>Files with 4_18_ in their name before the BDJ or VDJ text correspond to the 18-month-old mouse that was processed and sequenced alone. </p> <p> </p> <p>The L001 - L004 in the file names indicates the sequencing lane. Samples with BDJ correspond to the B cell repertoire library (B cell VDJ). Samples with TDJ correspond to the T cell repertoire library (T cell VDJ). </p>
Supporting data for "Dynamics of RNA polymerase II and elongation factor Spt4/5 recruitment during activator-dependent transcription"
<p>Supporting data for</p> <p><strong>Dynamics of RNA polymerase II and elongation factor Spt4/5 recruitment</strong></p> <p><strong>during activator-dependent transcription </strong></p> <p>Grace A. Rosen<sup>a,1</sup>, Inwha Baek<sup>b,1</sup>, Larry J. Friedman<sup>a</sup>, Yoo Jin Joo<sup>b</sup>, Stephen Buratowski<sup>b,2</sup>, Jeff Gelles<sup>a,2</sup></p> <p><sup>a</sup>Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454, USA.</p> <p><sup>b</sup>Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.</p> <p><sup>1</sup>Equal contributions</p> <p><sup>2</sup>Corresponding authors: <a href="mailto:steveb@hms.harvard.edu">steveb@hms.harvard.edu</a>; +1 (617) 432-0696 (S.B.) and <a href="mailto:gelles@brandeis.edu">gelles@brandeis.edu</a>; +1 (781) 736-2377 (J.G.)</p> <p>See <strong>Source data index.pdf</strong> for description of files.</p>
Transcription regulator ACTR contributes pathogenicity through mediating ACT toxin synthesis gene ACTS4 in Alternaria alternata
<p>Host-selective ACT toxin are critical for the pathogenesis of the citrus fungal pathogen <em>Alternaria alternata</em>. The biosynthesis of ACT toxin is mainly regulated by multiple ACT toxin genes located in the secondary metabolite gene cluster. However, the regulatory hierarchy of ACT toxin synthesis by these ACT genes have not been explored. In this study, we reported a transcription regulator <em>ACTR</em> contributes ACT toxin biosynthesis through mediating ACT toxin synthesis gene ACTS4 in <em>Alternaria alternata.</em> We generated <em>ACTR</em>-disrupted and -silenced mutants in the tangerine pathotype of <em>A. alternata.</em> Phenotype analysis showed that the <em>ACTR</em> mutants displayed a significant loss of ACT toxin production and a decreased virulence on citrus leaves whereas the vegetative growth and sporulation were not affected, indicating an essential role of <em>ACTR</em> in both ACT toxin biosynthesis and pathogenicity. To elucidate the transcription network of ACTR, we performed RNA-Seq experiments on wild-type and <em>ACTR</em> null mutant and identified genes that were differentially expressed between two genotypes. Transcriptome profiling and RT-qPCR analysis demonstrated that the ACT toxin biosynthetic gene <em>ACTS4</em> is down-regulated in<em> ACTR </em>mutant<em>.</em> We generated <em>ACTS4 </em>knock-down mutant and found that the pathogenicity of <em>ACTS4</em> mutant was severely impaired. Interestingly, both <em>ACTR</em> and <em>ACTS4</em> are not involved in the response to different abiotic stresses including oxidative stress, salt stress, cell-wall disrupting regents, and Cu<sup>2+</sup>, indicating the function of these two genes is highly specific. In conclusion, our results highlight the important regulatory role of <em>ACTR</em> in ACT toxin biosynthesis through mediating ACT toxin synthesis gene ACTS4 and underline the essential role of in the tangerine pathotype of <em>A. alternata</em>.</p>
LERC: Linked Extended Regulatory Circuits dataset on interactions between transcription factors and genes
<p>Turtles files of the project: <a href="https://regulatorycircuits-lod.genouest.org/">https://regulatorycircuits-lod.genouest.org/</a><br> 808 samples-specific files<br> 394 tissues-specific files<br> 2 mapping (FMA and Uberon)<br> 1 graph of experimental context<br> 1 graph of metadata</p> <p> </p>
A single-parasite transcriptional atlas of Toxoplasma gondii reveals novel control of antigen expression
Toxoplasma gondii, a protozoan parasite, undergoes a complex and poorly understood developmental process that is critical for establishing a chronic infection in its intermediate hosts. Here, we applied single-cell RNA-sequencing (scRNA-seq) on >5,400 Toxoplasma in both tachyzoite and bradyzoite stages using three widely studied strains to construct a comprehensive atlas of cell-cycle and asexual development, revealing hidden states and transcriptional factors associated with each developmental stage. Analysis of SAG1-related sequence (SRS) antigenic repertoire reveals a highly heterogeneous, sporadic expression pattern unexplained by measurement noise, cell cycle, or asexual development. Furthermore, we identified AP2 IX-1 as a transcription factor that controls the switching from the ubiquitous SAG1 to rare surface antigens not previously observed in tachyzoites. In addition, comparative analysis between Toxoplasma and Plasmodium scRNA-seq results reveals concerted expression of gene sets, despite fundamental differences in cell division. Lastly, we built an interactive data-browser for visualization of our atlas resource.
Data from: Divergent transcriptional patterns are related to differences in hypoxia tolerance between the intertidal and the subtidal sculpins
Transcriptionally mediated phenotypic plasticity as a mechanism of modifying traits in response to an environmental challenge remains an important area of study. We compared the transcriptional responses to low-oxygen (hypoxia) of the hypoxia tolerant intertidal fish, the tidepool sculpin (Oligocottus maculosus) with the closely related hypoxia intolerant subtidal fish, the silverspotted sculpin (Blepsias cirrhosus) to determine if these species use different mechanisms to cope with hypoxia. Individuals from each species were exposed to environmental O2 tensions chosen to yield a similar level of tissue hypoxia and gene transcription was assessed in the liver over time. There was an effect of time in hypoxia, where the greatest transcriptional change in the silverspotted sculpin occurred between 3 to 24 hours in contrast to the tidepool sculpin where the largest transcriptional change occurred between 24 and 72 hours of hypoxia. A number of genes showed similar hypoxia-induced transcription patterns in both species (e.g. genes associated with glycolysis and apoptosis) suggesting they are involved in a conserved hypoxia response. A large set of genes showed divergent transcriptional patterns in the two species, including fatty acid oxidation and oxidative phosphorylation, suggesting that these biological processes may contribute to explaining variation in hypoxia tolerance in these species. When both species were exposed to a single environmental O2 tension, large transcriptional responses were seen in the hypoxia intolerant silverspotted sculpin while almost no response was observed in the hypoxia tolerant tidepool sculpin. Overall, divergent transcription patterns in response to both magnitude and duration of hypoxia provide insights into the processes that may determine an animal's capacity to tolerate frequent bouts of hypoxia in the wild.
Data from: The transcriptional landscape of seasonal coat colour moult in the snowshoe hare
Seasonal coat colour change is an important adaptation to seasonally changing environments but the evolution of this and other circannual traits remains poorly understood. In this study we use gene expression to understand seasonal coat colour moulting in wild snowshoe hares (Lepus americanus). We used hair colour to follow the progression of the moult, simultaneously sampling skin from three moulting stages in hares collected during the peak of the spring moult from white winter to brown summer pelage. Using RNA-sequencing, we tested if patterns of expression were consistent with predictions based on the established phases of the hair growth cycle. We found functionally consistent clustering across skin types, with 766 genes differentially expressed between moult stages. "White" pelage showed more differentially expressed genes that were upregulated relative to other skin types, involved in the transition between late telogen (quiescent stage) and the onset of anagen (proliferative stage). Skin samples from transitional "intermediate" and "brown" pelage were transcriptionally similar and resembled the regressive transition to catagen (regressive stage). We also detected differential expression of several key circadian clock and pigmentation genes, providing important means to dissect the bases of alternate seasonal colour morphs. Our results reveal that pelage colour is a useful biomarker for seasonal change but that there is a consistent lag between the main gene expression waves and change in visible coat colour. These experiments establish that developmental sampling from natural populations of non-model organisms can provide a crucial resource to dissect the genetic basis and evolution of complex seasonally changing traits.
Data from: A clinal polymorphism in the insulin signaling transcription factor foxo contributes to life-history adaptation in Drosophila
A fundamental aim of adaptation genomics is to identify polymorphisms that underpin variation in fitness traits. In D. melanogaster latitudinal life-history clines exist on multiple continents and make an excellent system for dissecting the genetics of adaptation. We have previously identified numerous clinal SNPs in insulin/insulin-like growth factor signaling (IIS), a pathway known from mutant studies to affect life history. However, the effects of natural variants in this pathway remain poorly understood. Here we investigate how two clinal alternative alleles at foxo, a transcriptional effector of IIS, affect fitness components (viability, size, starvation resistance, fat content). We assessed this polymorphism from the North American cline by reconstituting outbred populations, fixed for either the low- or high-latitude allele, from inbred DGRP lines. Since diet and temperature modulate IIS, we phenotyped alleles across two temperatures (18°C, 25°C) and two diets differing in sugar source and content. Consistent with clinal expectations, the high-latitude allele conferred larger body size and reduced wing loading. Alleles also differed in starvation resistance and expression of InR, a transcriptional target of FOXO. Allelic reaction norms were mostly parallel, with few GxE interactions. Together, our results suggest that variation in IIS makes a major contribution to clinal life-history adaptation.
Elearning study Transcript Dataset
<p>Transcripts of three focus groups with medical students about their experiences of engaging with elearning materials</p>
Transcriptional decomposition reveals active chromatin architectures and cell specific regulatory interactions
<p><strong>Summary</strong></p> <p>Resource data across the 76 cell types from FANTOM5 analysed in our paper titled "Transcriptional decomposition reveals active chromatin architectures and cell specific regulatory interactions".</p> <p><strong>Project abstract</strong></p> <p>Gene transcription is influenced by favourable chromosome positioning and chromatin architectures bringing regulatory elements in close proximity. However, it is unclear to what extent transcription is attributable to topological organisation or to gene-specific regulatory programs. Here, we develop a strategy to transcriptionally decompose expression data into two main components reflecting the positional relationship of neighbouring transcriptional units and effects independent from their positioning. </p> <p>We demonstrate that the positionally dependent component is highly informative of topological domain activity and organisation, revealing boundaries and chromatin compartments. Furthermore, features derived from transcriptional components can accurately predict individual chromatin interactions. We systematically investigate regulatory interactions and observe different transcriptional attributes governing long- and short-range interactions. Finally, we assess differences in regulatory organisations across 76 human cell types. In all, we demonstrate a close relationship between transcription and topological chromatin architecture and provide an unprecedented resource for investigations of regulatory organisations across cell types.</p> <p><strong>Included files</strong></p> <p>PD_component_76_cell_types.tar.gz - Contains the positionally dependent (PD) components for 76 human cell types.</p> <p>PD_sd_component_76_cell_types.tar.gz - Contains the standard deviations of the positionally dependent (PD_sd) components for 76 human cell types.</p> <p>PI_component_76_cell_types.tar.gz - Contains the positionally independent (PI) components for 76 human cell types.</p> <p>PI_sd_component_76_cell_types.tar.gz - Contains the standard deviations of the positionally independent (PI_sd) components for 76 human cell types.</p> <p>predicted_EP_interactions_76_cell_types.tar.gz - Contains predicted enhancer-promoter interactions for 76 human cell types.</p> <p>predicted_boundaries_76CT.txt - Matrix with 76 columns representing human cell types and 10kb genome-wide bins as rows, coded as 0 or 1 according to whether a XAD boundary was predicted in the bin for a given cell type.</p>
Photos of ostraca of Iruña-Veleia (Spain) with scale and transcription.
<p>Photos of ostraca of Iruña-Veleia (Spain) with scale and transcription in the article by Joseba Lizeaga.</p>
Transcripts of 28 interviews with researchers who fabricated data for an experiment
<p>For an experiment we recently conducted, we asked researchers to fabricate data for a Stroop experiment. The purpose of this experiment was to test whether we could use statistics to discern the fabricated data from genuine data we collected from Many Labs 3. We also interviewed the researchers about how they fabricated data, in order to learn how researchers actually fabricate data. We share these transcripts here for maximum reuse under a CC 0 license.</p> <p> </p>
Anonymized Transcripts of Change Laboratory Workshops
<p>Full transcript in Italian of the Change laboratory workshops in a a secondary vocational secondary institute in the Lombardy region.</p> <p>The workshops involved an overall number of 37 participants throughout the meetings between humanity teachers, science teachers, technical teachers and workshop assistants. </p> <p>Transcripts of 7 workshops (in 2016), 2 follow-up and two department councils (in 2016 and 2017). </p> <p>The transcripts have been fully anonymized.</p> <p> </p>
Transcripts of expert interviews with writing center directors in the USA in 2012
<p>This document contains transcripts of interviews with 16 writing center directors in different writing centers in the USA, conducted in 2012. The overall research question for the interviews was how writing center directors deal with challenges in writing center work and how they conduct institutional work for their writing centers.</p> <p>The interviews belong to the habilitation thesis <em>“Strategien für die Institutionalisierung von Schreibzentren an Hochschulen. Eine qualitative Analyse der Institutionalisierungsarbeit von Leitungspersonen in Schreibzentren“</em>, as proposed to the <em>Fakultätsrat der Kultur-, Sozial- und Bildungswissenschaftlichen Fakultät</em> of the Humboldt University Berlin, April 1st 2016. The study has been accepted as habilitation by the <em>Fakultätsrat</em> at February 15<sup>th</sup> 2017.</p> <p>The results of the study will be published as open access publication (e-book) and in print by W.Bertelsmann Verlag (wbv) Bielefeld in October 2017. The study contains a description of demographic details and other details of the interviews and explains the methodology, which clarifies why the interview transcripts eventually change to part-transcriptions due to theoretical saturation.</p> <p> </p>
Dissection of core promoter syntax through single nucleotide resolution modeling of transcription initiation (CLIPNET data)
<div>This contains data necessary to reproduce the figures in the CLIPNET paper (preprint <a href="https://www.biorxiv.org/content/10.1101/2024.03.13.583868">here</a>) as well as processed data used to train and evaluate CLIPNET. To preserve subdirectory structure, we've packaged the data into tar archives. Please refer to the README documents in our manuscript GitHub repo for more details on file contents: <a href="https://github.com/Danko-Lab/clipnet_paper/">https://github.com/Danko-Lab/clipnet_paper/</a></div> <div> </div> <div>Pretrained CLIPNET models are archived separately at <a href="../doi/10.5281/zenodo.10408622">DOI 10.5281/zenodo.10408622</a></div> <div> </div> <div>V5: Fixed bug in calculation of profile attribution scores causing them to be off by a factor of exactly 500. Genome-wide DeepSHAP tracks & TF-MoDISco tracks have been accordingly updated. I have not updated the individual examples, as these can be quickly fixed by simply multiplying by 500 when plotting. Additionally, I have uploaded profile and quantity motif calls, which contain genome-wide seqlet annotations. The columns in these files are [chrom, start, end, peak_idx, motif_annotation].</div> <div>V4: Uploaded individual bigWigs. These have been lifted over using CrossMap from the original hg19 (GSE110638) to hg38 and RPM normalized.</div> <div>V3: Final version prior to journal submission. Don't recall exact details of what's changed.</div> <div>V2: evaluation_metrics.tar.gz and evaluation_data.tar.gz have been replaced. Previously, we benchmarked the models by treating each peak in each individual as a separate data point. Here, we instead predicted from the reference genome and compared against the averaged bigWigs.</div>
IPA Transcription and Recordings
<p>This file provides transcription of dialects data using IPA found in ten survey sites in West Manggarai, East Nusa Tenggara, Indonesia.</p>
Dataset for "Antisense transcription from neighboring genes interferes with the expression of mNeonGreen as a functional in vivo fluorescent reporter in the chloroplast of Chlamydomonas reinhardtii."
<p>Plasmid sequences for "Antisense transcription from neighboring genes interferes with the expression of mNeonGreen as a functional in vivo fluorescent reporter in the chloroplast of Chlamydomonas reinhardtii."</p>
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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.
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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.
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