Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
21,320
datasets available to search
ShareScore release 0.9.0
Dataset results
21,320 results for “Transcription”
Transcriptional determinants of lipid mobilization in human adipocytes
Open the record for dataset details and reuse information.
DoubleChEC program to identify transcription factor binding sites from mapped ChEC-seq data
Open the record for dataset details and reuse information.
Transcription start site analysis for heterogenous CD4+ T cells using 5′ scRNA-seq
Open the record for dataset details and reuse information.
Transcriptional regulation underlying the temperature response of embryonic development rate in the winter moth
Open the record for dataset details and reuse information.
Dataset for: Ultrarapid detection of SARS-CoV-2 RNA using a reverse transcription-free exponential amplification reaction, RTF-EXPAR
Open the record for dataset details and reuse information.
Post-transcriptional splicing can occur in a slow-moving zone around the gene
Open the record for dataset details and reuse information.
Quantitative modulation of a spatial enhancer through the biophysical properties of a transcription factor binding site
Open the record for dataset details and reuse information.
Simulations of gene regulatory networks with transcriptional adaptation
Open the record for dataset details and reuse information.
The interplay between prior selection, mild intermittent exposure, and acute severe exposure in phenotypic and transcriptional response to hypoxia
Open the record for dataset details and reuse information.
Data from: Whole blood transcriptional profiles and the pathogenesis of tuberculous meningitis
Open the record for dataset details and reuse information.
Data from: Deep mutational scanning of HBV reveals a mechanism for cis preferential reverse transcription
Open the record for dataset details and reuse information.
Data from: FSHB transcription is regulated by a novel 5’ distal enhancer containing a fertility-associated single nucleotide polymorphism
Open the record for dataset details and reuse information.
Distinct roles for H4 and H2A.Z acetylation in RNA transcription in African trypanosomes
<p>This repository contains the run scripts for this publication.</p> <p><strong>Complete data download</strong><br> http://resources-molpara.vetmed.lmu.de/Kraus_et_al_2019_sequencing_analysis.tar.gz</p> <p><strong>Contents of the tar.gz archive:</strong><br> upload_sequencing/<br> ├── bin/<br> │ ├── scripts necessary to run the pipeline<br> ├── input/<br> │ ├── input files<br> ├── output/<br> │ ├── output files for ChIP and RNA-seq<br> └── output2/<br> └── output files for ATAC-seq</p> <p><strong>Abstract</strong><br> Despite histone H2A variants and acetylation of histones occurring in almost every eukaryotic organism, it has been difficult to establish direct functional links between canonical histone or H2A variant acetylation, deposition of H2A variants and transcription. To disentangle these complex interdependent processes, we devised a highly sensitive strategy for quantifying histone acetylation levels at specific genomic loci. Taking advantage of the unusual genome organization in <em>Trypanosoma brucei</em>, we identify 58 histone modifications enriched at transcription start sites (TSSs). Furthermore, we find TSS-associated H4 and H2A.Z acetylation to be mediated by two different histone acetyltransferases, HAT2 and HAT1, respectively. Whereas depletion of HAT2 decreases H2A.Z deposition and shifts the site of transcription initiation, depletion of HAT1 does not affect H2A.Z deposition but reduces total mRNA levels by 50%. Thus, specifically reducing H4 or H2A.Z acetylation levels enabled us to reveal distinct roles for these modifications in H2A.Z deposition and RNA transcription.</p>
Annotated genes harboring major effect markers (R2 ≥ 15%). Highlighted in green are genes annotated from Rhodes et al. 2014,2017, in orange genes annotated as similar to Peroxidase, in yellow new annotations from sorghum genome in Atlas. In the first three columns start and stop position on the sorghum genome and transcript name, followed by the nearest marker name and the distance of the gene from the nearest marker, then a column where are shown the GWAS methods and target traits for which the linked SNP was significant, the last column shows the category of the genes.
<p><strong>We conducted a comprehensive genomics study to map genomic loci determining the production of antioxidants in sorghum grains. Encouraging results were obtained and published in peer-reviewed article with impact factor (https://doi.org/10.1371/journal.pone.0225979). Annotated genes harboring major effect markers (R<sup>2</sup> ≥ 15%) were identified and will be of worldwide interest. </strong></p>
Data for the paper "Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study".
<p>Data for the paper "Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study".</p>
Chinese transcriptions of Indic terms in the translations of Ān Shìgāo 安世高 and Lokakṣema 支婁迦讖
<p>This dataset includes the Chinese transcriptions of Indic terms in the translations of Ān Shìgāo 安世高 and Lokakṣema 支婁迦讖. The coverage of of Ān Shìgāo complete, except for the two Kongōji manuscripts not included in the Taishō canon. The coverage of Lokakṣema is less systematic, including what is indexed by Karashima (2010) from the <em><em>Aṣṭasāhasrikā Prajñāpāramitā</em></em> and what was included in Coblin's (1983) study.</p> <p>Coblin, W. South (1983). <em>A handbook of Eastern Han sound glosses</em>. Hong Kong: Chinese University Press.</p> <p>Karashima, Seishi (2010). <em>A glossary of Lokakṣema's translation of the Aṣṭasāhasrikā Prajñāpāramit</em>ā. (Bibliotheca philologica et philosophica buddhica 11). Tokyo : International Research Institute for Advanced Buddhology, Soka University, 2010.</p> <p> </p> <p> </p>
Videos of live transcription of T48 in D. melanogaster during nuclear cycle 14
<p>Videos showing live imaging of transcription of T48 (green) at the start of nuclear cycle 14 in developing embryos of <em>Drosophila melanogaster</em>. Video names indicate the enhancer allele used, and the number in the name indicates the replicate number.</p>
The transcription regulatory code of a plant leaf
<p>The transcription regulatory network underlying essential and complex functionalities inside a eukaryotic cell is defined by the combinatorial actions of transcription factors (TFs). However, TF binding studies in plants are too few in number to produce a general and comparative picture of this complex regulatory network. Here, we used ChIP-seq to determine the binding profiles of 104 TF expressed in the maize leaf (Data can be downloaded from NCBI SRA under accession number PRJNA518749) </p> <p>With this large dataset, we trained machine-learning models to identify TF sequence preferences. A contrast between Maize and Arabidopsis TF sequence preferences revealed that DNA binding follows the conservation of TF protein families. Finally, the trained models were used to predict and compare the regulatory networks in other grasses species (Sorghum and Rice), which revealed that the edges between TF and TF coding genes are more likely to be maintained (<em>i.e., </em>evolutionarily conserved). </p> <p>On a practical level, we expect the presented TF binding models to be integrated into pipelines to predict effects of non-coding variants, both common and rare, on TF binding, to pinpoint causal sites. As the possibility of being able to predict and generate novel variation not seen in nature could fundamentally change future plant breeding.</p> <p>Detail: Each *tar.gz file is a <strong><a href="https://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-019-1693-2">bag-of-k-mer model</a></strong> fitted for a single ZmTF, which can be used for predictions. Information about each ZmTF is included in the table tfids.tsv</p> <p>For more information about the project: <br> <a href="https://www.biorxiv.org/content/10.1101/2020.01.07.898056v3"><strong>The transcription regulatory code of a plant leaf</strong></a></p>
Data from: Cre-mediated, loxP independent sequential recombination of a tripartite transcriptional stop cassette allows for partial read-through transcription
<p>One of the widely used applications of the popular Cre-loxP method for targeted recombination is the permanent activation of marker genes, such as reporter genes or antibiotic resistance genes, by excision of a preceding transcriptional stop signal. The STOP cassette consists of three identical SV40-derived poly(A) signal repeats and is flanked by two loxP sites. We found that in addition to complete loxP-mediated recombination, limiting levels of the Cre recombinase also cause incomplete recombination of the STOP cassette. Partial recombination leads to the loss of only one or two of the three identical poly(A) repeats with recombination breakpoints always precisely matching the end/start of each poly(A) signal repeat without any relevant similarity to the canonical or known cryptic loxP sequences, suggesting that this type of Cre-mediated recombination is loxP-independent. Incomplete deletion of the STOP cassette results in partial read-through transcription, explaining at least some of the variability often observed in marker gene expression from an otherwise identical locus.</p>
Inscription of Čơṅ Aṅ : Transcription, translation and analysis.
<p>Philip Jenner, <a href="https://siddham.network/inscription/k99/">K.99</a> Inscription of Čơṅ Aṅ : Transcription, translation and analysis.</p> <p><a href="https://catalog.lib.uchicago.edu/vufind/alphabrowse/home?source=topic&from=Inscriptions+--+Cambodia">Inscriptions -- Cambodia</a><br> <a href="https://catalog.lib.uchicago.edu/vufind/alphabrowse/home?source=topic&from=Inscriptions.">Inscriptions. </a><br> <a href="https://catalog.lib.uchicago.edu/vufind/alphabrowse/home?source=topic&from=Cambodia.">Cambodia. </a></p>
ScienceDex guides
Understand access before you commit
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.