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.
3,291
datasets available to search
ShareScore release 0.9.0
Dataset results
3,291 results for “transcription regulation”
Differential analysis of gene regulation at transcript resolution by RNA-Seqcount table
<p>Expression profiling by high throughput sequencing</p>
Data from: Phenotypic plasticity through transcriptional regulation of the evolutionary hotspot gene tan in Drosophila melanogaster
Phenotypic plasticity is the ability of a given genotype to produce different phenotypes in response to distinct environmental conditions. Phenotypic plasticity can be adaptive. Furthermore, it is thought to facilitate evolution. Although phenotypic plasticity is a widespread phenomenon, its molecular mechanisms are only beginning to be unravelled. Environmental conditions can affect gene expression through modification of chromatin structure, mainly via histone modifications, nucleosome remodelling or DNA methylation, suggesting that phenotypic plasticity might partly be due to chromatin plasticity. As a model of phenotypic plasticity, we study abdominal pigmentation of Drosophila melanogaster females, which is temperature sensitive. Abdominal pigmentation is indeed darker in females grown at 18°C than at 29°C. This phenomenon is thought to be adaptive as the dark pigmentation produced at lower temperature increases body temperature. We show here that temperature modulates the expression of tan (t), a pigmentation gene involved in melanin production. t is expressed 7 times more at 18°C than at 29°C in female abdominal epidermis. Genetic experiments show that modulation of t expression by temperature is essential for female abdominal pigmentation plasticity. Temperature modulates the activity of an enhancer of t without modifying compaction of its chromatin or level of the active histone mark H3K27ac. By contrast, the active mark H3K4me3 on the t promoter is strongly modulated by temperature. The H3K4 methyl-transferase involved in this process is likely Trithorax, as we show that it regulates t expression and the H3K4me3 level on the t promoter and also participates in female pigmentation and its plasticity. Interestingly, t was previously shown to be involved in inter-individual variation of female abdominal pigmentation in Drosophila melanogaster, and in abdominal pigmentation divergence between Drosophila species. Sensitivity of t expression to environmental conditions might therefore give more substrate for selection, explaining why this gene has frequently been involved in evolution of pigmentation.
The transcription factor PagLBD3 contributes to the regulation of secondary growth in Populus
<p>Lateral organ boundaries domain (LBD) genes encode plant-specific transcription factors that participate in regulating various developmental processes. In this study, we genetically characterized PagLBD3 as an important regulator of secondary growth in Populus. Overexpression of PagLBD3 increased stem secondary growth in Populus with significantly higher rate of cambial cells differentiated into phloem, while dominant repression of PagLBD3 significantly decreased the rate of cambial cells differentiated into phloem. Furthermore, we identified 1756 PagLBD3 genome-wide putative direct target genes (DTGs) through RNA sequencing (RNA-seq) coupled DNA affinity purification followed by sequencing (DAP-seq) assays. Gene Ontology analysis revealed that genes regulated by PagLBD3 were enriched in biological pathways regulating meristem development, xylem development, and auxin transport. Several central regulator genes for vascular development, including phloem intercalated with xylem (PXY), wuschel related homeobox4 (WOX4), Secondary Wall-Associated NAC Domain 1s (SND1-B2) and Vascular-Related NAC-Domain 6s (VND6-B1), were identified as PagLBD3 DTGs. Together, our results suggested that PagLBD3 and its DTGs form a complex transcriptional network to modulate cambium activity and phloem/xylem differentiation.</p>
Titrating Avidity of Yeast-Displayed Proteins Using a Transcriptional Regulator
<p>Data underlying the figures in the publication: Lopez-Morales, J. <em>et al.</em> “Titrating Avidity of Yeast-Displayed Proteins Using a Transcriptional Regulator” <em>ACS Synth. Biol.</em> <strong>2023</strong>, <em>12</em>, 419-31, <a href="https://doi.org/10.1021/acssynbio.2c00351">https://doi.org/10.1021/acssynbio.2c00351</a></p> <p><strong>Table of Contents</strong></p> <p><strong>Fig1_subplots_EMpty pJL100 full atc range analysis.xlsx:</strong> Flow cytometry data of displaying fraction and median fluorescence for Fig. 1c and d.</p> <p><strong>Fig2_subplots_20.08.05 tit disp GOx ABTS.xlsx:</strong> Flow cytometry data of displaying fraction and median fluorescence of Gox variants; GOX enzymatic activity assay data for Fig. 2</p> <p><strong>Fig3_subplots_ SDA data for sharing.xlsx and disks + sup data plot.pptx:</strong> Spinning disk assay data and micrographs for Fig. 3.</p> <p><strong>Fig4_ subplots_20220421 YTD affibody aTc vs Gal titration curves.xlsx and 20220423 Gal good volume.xlsx: </strong>Flow cytometry data and PDL1 titration on yeast data for Fig. 4.</p> <p><strong>Supplementary_Gal comparison_</strong> <strong>Gal time point-2.xlsx: </strong>Flow cytometry data for comparing the YTD system to the standard yeast surface display for sup. Fig. S1.</p> <p><strong>Supplementary_Fig S3_Titrated Affibody Kd analysis.xlsx and Simulations.pzf:</strong> ICE tables and simulation spreadsheet for sup. Fig. S3.</p>
Transcriptional profiling of the response to starvation and fattening reveals differential regulation of autophagy genes in mammals
<p>Nutrient deprivation (starvation) induced by fasting and hypercaloric regimens are stress factors that can influence cell and tissue homeostasis in mammals. One of the key cellular responses to changes in nutrient availability is the cell survival pathway, autophagy. While there has been much research into the protein networks regulating autophagy, less is known about the gene expression networks involved in this fundamental process. Here, we applied a network algorithm designed to analyze omics datasets, to identify sub-networks that are enriched for induced genes in response to starvation. This enabled us to identify two prominent active modules composed of key stress-induced transcription factors, including members of the Jun, Fos, and ATF families, and the other comprising autophagosome sub-network genes, including ULK1. The results were validated in the brain, liver, and muscle of fasting mice. Moreover, differential expression analysis of autophagy genes in the brain, liver, and muscle of high-fat diet-exposed mice, showed significant suppression of GABARAPL1 in the liver. Finally, our data provide a resource that may facilitate the future identification of regulators of autophagy.</p>
Transcriptional profiling of the response to starvation and fattening reveals differential regulation of autophagy genes in mammals
Open the record for dataset details and reuse information.
Data from: Positive selection within a diatom species acts on putative protein interactions and transcriptional regulation
Open the record for dataset details and reuse information.
The transcription factor PagLBD3 contributes to the regulation of secondary growth in Populus
Open the record for dataset details and reuse information.
Data from: Limits on information transduction through amplitude and frequency regulation of transcription factor activity
Open the record for dataset details and reuse information.
Data from: Quantitative proteomics reveals key roles for post-transcriptional gene regulation in the molecular pathology of FSHD
Open the record for dataset details and reuse information.
Data from: Phenotypic plasticity through transcriptional regulation of the evolutionary hotspot gene tan in Drosophila melanogaster
Open the record for dataset details and reuse information.
Raw data related to: "Transcriptional Regulators of T Helper 17 Cell Differentiation in Health and Autoimmune Diseases"
<p><strong>Introduction</strong></p> <p>T helper (Th) 17 cells are a subtype of CD4 T lymphocytes characterized by the expression of retinoic acid-receptor (RAR)-related orphan receptor (ROR)γt transcription factor, encoded by gene <em>Rorc</em>. These cells are implicated in the pathology of autoimmune inflammatory disorders as well as in the clearance of extracellular infections. The main function of Th17 cells is the production of cytokine called interleukin (IL)-17A.</p> <p><strong>Methods</strong></p> <p>We described the lineage defining transcription factor RORγt and other factors that regulate transcription of <em>Il17a, Rorc </em>and Th17-related genes, such as Il17f, Il21, Il23r, which may positively or negatively influence their expression.</p> <p><strong>Results</strong></p> <p>We discussed the potential new therapeutic approaches for Th17-related diseases targeting these transcription factors. The wide knowledge of transcriptional regulators of Th17 cells is crucial for the better understanding of the pathogenic role of these cells and for development of therapeutic strategies aimed at fighting Th17-related diseases.</p>
Data from: Diurnal transcriptional regulation of endosymbiotically derived genes in the chlorarachniophyte Bigelowiella natans
Chlorarachniophyte algae possess complex plastids acquired by the secondary endosymbiosis of a green alga, and the plastids harbor a relict nucleus of the endosymbiont, the so-called nucleomorph. Due to massive gene transfer from the endosymbiont to the host, many proteins involved in plastid and nucleomorph are encoded by the nuclear genome. Genome sequences have provided a blueprint for the fate of endosymbiotically derived genes; however, transcriptional regulation of these genes remains poorly understood. To gain insight into the evolution of endosymbiotic genes, we performed genome-wide transcript profiling along the cell cycle of the chlorarachniophyte Bigelowiella natans, synchronized by light and dark cycles. Our comparative analyses demonstrated that transcript levels of 7,751 nuclear genes (35.7% of 21,706 genes) significantly oscillated along the diurnal/cell cycles, and those included 780 and 147 genes for putative plastid and nucleomorph-targeted proteins, respectively. Clustering analysis of those genes revealed the existence of transcriptional networks related to specific biological processes such as photosynthesis, carbon metabolism, translation, and DNA replication. Interestingly, transcripts of many plastid-targeted proteins in B. natans were induced before dawn, unlike other photosynthetic organisms. In contrast to nuclear genes, 99% nucleomorph genes were found to be constitutively expressed during the cycles. We also found that the nucleomorph DNA replication would be controlled by a nucleus-encoded viral-like DNA polymerase. The results of this study suggest that nucleomorph genes have lost transcriptional regulation along the diurnal cycles, and nuclear genes exert control over the complex plastid including the nucleomorph.
Data from: Nod factors potentiate auxin signaling for transcriptional regulation and lateral root formation in Medicago truncatula
Nodulation (Nod) factors (NFs) are symbiotic molecules produced by rhizobia that are essential for establishment of the rhizobium–legume endosymbiosis. Purified NFs can stimulate lateral root formation (LRF) in Medicago truncatula, but little is known about the molecular mechanisms involved. Using a combination of reporter constructs, pharmacological and genetic approaches, we show that NFs act on early steps of LRF in M. truncatula, independently of the ethylene signaling pathway and of the cytokinin receptor MtCRE1, but in interaction with auxin. We conducted a whole-genome transcriptomic study upon NF and/or auxin treatments, using a lateral root inducible system adapted for M. truncatula. This revealed a large overlap between NF and auxin signaling and, more interestingly, synergistic interactions between these molecules. Three groups showing interaction effects were defined: group 1 contained more than 1500 genes responding specifically to the combinatorial treatment of NFs and auxin; group 2 comprised auxin-regulated genes whose expression was enhanced or antagonized by NFs; and in group 3 the expression of NF regulated genes was antagonized by auxin. Groups 1 and 2 were enriched in signaling and metabolic functions, which highlights important crosstalk between NF and auxin signaling for both developmental and symbiotic processes.
Inference of molecular mechanisms of transcriptional regulation from co-expression data
<p>The accompanying data for the article "Inference of molecular mechanisms of transcriptional regulation from co-expression data". The article is now live on Research Square <a href="https://doi.org/10.21203/rs.3.rs-1262163/v1">10.21203/rs.3.rs-1262163/v1</a></p>
The novel regulator HdrR controls the transcription of the heterodisulfide reductase operon hdrBCA in Methanosarcina barkeri
<p><span>RNA-seq raw data and processed data are accessible at Zenodo.</span></p>
Multimodal single-cell analyses reveal distinct fusion-regulated transcriptional programs in Ewing sarcoma.
<p>All processed data for analysis at <a href="https://github.com/furlan-lab/EwS_multiome">https://github.com/furlan-lab/EwS_multiome</a></p>
Data for Single-molecule Detection of Modified Amino Acid Regulating Transcriptional Activity
Open the record for dataset details and reuse information.
Rice genome-scale network integration reveals transcriptional regulators of grass cell wall synthesis
<p><span><span><span><span><span><span><span><span><span><span><span>Grasses have evolved distinct cell wall composition and patterning relative to dicotyledonous plants. However, despite the importance of this plant family, transcriptional regulation of its cell wall biosynthesis is poorly understood. To identify grass cell wall-associated transcription factors, we constructed the Rice Combined mutual Ranked Network (RCRN). The RCRN covers >90% of annotated rice (<i>Oryza sativa</i>) genes, is high quality, and includes most grass-specific cell wall genes, such as mixed-linkage glucan synthases and hydroxycinnamoyl acyltransferases. Comparing the RCRN and an equivalent <i>Arabidopsis </i>network suggests that grass orthologs of most genetically verified eudicot cell wall regulators also control this process in grasses, but some vary significantly in network connectivity between these divergent species. Reverse genetics, yeast-one-hybrid, and protoplast-based assays reveal that OsMYB61a activates a grass-specific acyltransferase promoter, which confirms network predictions and supports grass-specific cell wall synthesis genes being incorporated into conserved regulatory circuits. In addition, 10 of 15 tested transcription factors, including six novel <u>w</u>all-<u>a</u>ssociated regulators (WAP1, WACH1, WAHL1, WADH1, OsMYB13a, and OsMYB13b), alter abundance of cell wall-related transcripts when transiently expressed. The results highlight the quality of the RCRN for examining rice biology, provide insight into the evolution of cell wall regulation, and identify network nodes and edges that are possible leads for improving cell wall composition.</span></span></span></span></span></span></span></span></span></span></span></p>
ArsR transcriptional regulator mediated attenuated mechanism by regulating self and outer membrane protein in Brucella
<p><span>The ArsR family transcriptional regulators are widely distributed in microorganisms, including in the important intracellular pathogen <i>Brucella</i>. ArsR proteins are implicated in numerous biological processes. However, the specific roles of ArsR family members in <i>Brucella</i> remain obscure. Here we show that ArsR3 (BSS2_RS07325) is required for <i>Brucella</i> survival both under stress <i>in vitro</i> conditions and in a murine infection model<i> in vivo</i>. ArsR3 autoregulate its own expression to maintain metal ion homeostasis to benefit bacterial survival. Moreover, ArsR3 also regulates the production of virulence factor outer membrane protein 25D (Omp25D) which is key for the survival of <i>Brucella</i> under stress conditions. Significantly, ArsR3 deletion strain attenuated in a murine infection model<i> in vivo</i>. Altogether, our findings reveal a unique mechanism in which the ArsR family member ArsR3 autoregulates its expression and also modulates Omp25D expression to maintain metal ion homeostasis and virulence in <i>Brucella</i>.</span></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.