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Dataset results
113 results for “signal sequence”
Dataset to the publication "A unique signal sequence of the chemokine receptor CCR7 promotes package into COPII vesicles for efficient receptor trafficking"
<p>This repository accompanies the paper:</p> <p>"A unique signal sequence of the chemokine receptor CCR7 promotes package into COPII vesicles for efficient receptor trafficking".</p> <p>Organized into 14 folders it provides the data allowing the replication of all analyses and the manuscript's figures. For a more convenient download files were zipped.</p> <p>Upon publication of results using this dataset, please cite the following paper:</p> <p>Uetz-von Allmen E, Rippl AV, Farhan H, Legler DF. 2018. A unique signal sequence of the chemokine receptor CCR7 promotes package into COPII vesicles for efficient receptor trafficking. J Leukoc Biol 104(2):375-389.</p>
Hybrid sequencing reveals insight into heat sensing and signaling of bread wheat
<p>Wheat (<em>Triticum aestivum</em> L.), a globally important crop, is challenged by increasing temperatures (heat stress, HS); however, its polyploid nature, the incompleteness of its genome sequences and annotation, the lack of comprehensive HS-responsive transcriptomes and the unexplored heat sensing and signaling of wheat hinder our full understanding of its adaptations to HS. The recently released genome sequences of wheat, as well as the emerging single-molecular sequencing technologies, provides an opportunity to thoroughly investigate the molecular mechanisms of the wheat response to HS. We generated a high-resolution spatio-temporal transcriptome map of wheat flag leaves and filling grain under HS at 0 minute (m), 5 m, 10 m, 30 m, 1 hour (h) and 4 h by combining full-length single-molecular sequencing and Illumina short reads sequencing. This hybrid sequencing newly discovered 4,947 loci and 70,285 transcripts, generating the comprehensive and dynamic list of HS-responsive full-length transcripts and complementing the recently released wheat reference genome.</p>
Data for: Beyond signal quality: The value of unmaintained pH, dissolved oxygen, and oxidation-reduction potential sensors for remote performance monitoring of on-site sequencing batch reactors
<p>Sensor maintenance is time-consuming and is a bottleneck for monitoring on-site wastewater treatment systems. Hence, we compare maintained and unmaintained sensors to monitor the biological performance of a small-scale sequencing batch reactor (SBR). The sensor types are ion-selective pH, optical dissolved oxygen (DO), and oxidation-reduction potential (ORP) with platinum electrode. We created soft sensors using engineered features: ammonium valley for pH, oxidation ramp for DO, and nitrite ramp for the ORP. Four soft sensors based on unmaintained pH sensors correctly identified the completion of the ammonium oxidation (89 to 91 out of 107 cycles), about as many times as soft sensors based on a maintained pH sensor (91 out of 107 cycles). In contrast, the DO soft sensor using data from a maintained sensor showed slightly better (89 out of 96 cycles) detection performance than that using data from two unmaintained sensors (77, respectively 82 out of 96 correct). Furthermore, the DO soft sensor using maintained data is much less sensitive to the optimisation of cut-off frequency and slope tolerance than the soft sensor using unmaintained data. The nitrite ramp provided no useful information on the state of nitrite oxidation, so no comparison of maintained and unmaintained ORP sensors was possible in this case. We identified two hurdles when designing soft sensors for unmaintained sensors: i) Sensors' type- and design-specific deterioration affects performance. ii) Feature engineering for soft sensors is sensor type specific, and the outcome is strongly influenced by operational parameters such as the aeration rate. In summary, the results with the provided soft sensors show that frequent sensor maintenance is not necessarily needed to monitor the performance of SBRs. Without sensor maintenance monitoring smalls-scale SBRs becomes practicable, which could improve the reliability of unstaffed on-site treatment systems substantially.</p>
Chronic social defeat stress induces meningeal neutrophilia via type I interferon signaling: single cell RNA sequencing data
<p>Meningeal single cell RNA sequencing data</p> <p>Meningeal samples were collected from both dorsal and ventral skull, avoiding inclusion of choroid plexus. Samples were digested in 2.5 mg/mL Collagenase D (Cat. #11088858001; Roche) and 12.5 μL of 0.5 mg/mL DNAseI (Cat. #L5002139; Worthington), put on a shaker at 370C for 30 m, diluted with cold HBSS + 0.1% BSA, and mashed through a 70 μm cell strainer prior to sorting.</p> <p>Data represent live, nucleated, singlet cells (DAPI-DRAQ5+) sorted on a BD FACS Aria Fusion into HBSS + 10% FBS prior to droplet encapsulation using 10x Genomics’ Drop-seq platform (Chromium v2).</p> <p>10X chip lane is indicate by 'group' column</p> <p>Group 1 = 4 pooled homecage control (unstressed) mice</p> <p>Group 2 = 4 pooled homecage control (unstressed) mice</p> <p>Group 3 = 4 pooled mice exposed to chronic social defeat for 14 days; tissue was collected 2 hours following final defeat</p> <p>See the following repositories for data processing:</p> <p><a href="https://github.com/maryellenlynall/2019_bcell_stress/blob/master/bcellstress20.Rmd">https://github.com/maryellenlynall/2019_bcell_stress/</a> (processing from raw files starts at bcellstress020.Rmd)</p> <p><a href="https://github.com/staceykigar/meningeal_neut/">https://github.com/staceykigar/meningeal_neut/</a></p> <p>We also provide a processed dataset (processed.RData) with assays 'counts' and 'logcounts' which is the processed single cell object saved at line "# Save object for upload to Zenodo" in script <a href="https://github.com/staceykigar/meningeal_neut/">https://github.com/staceykigar/meningeal_neut/</a>neutrophilstress01.Rmd </p> <p>Cluster annotations are in sce$Annotation</p> <p>Neutrophil subcluster annotations are in sce$Subcluster</p> <p>Sample condition is in sce$cond, where "HC" indicates homecage control and "SD" indicates chronic social defeat</p> <p>10X chip lane is in sce$group</p>
Data from: Parallel mechanisms signal a hierarchy of sequence structure violations in the auditory cortex
<p>The brain predicts regularities in sensory inputs at multiple complexity levels, with neuronal mechanisms that remain elusive. Here, we monitored auditory cortex activity during the local-global paradigm, a protocol nesting different regularity levels in sound sequences. We observed that mice encode local predictions based on stimulus occurrence and stimulus transition probabilities, because auditory responses are boosted upon prediction violation. This boosting was due to both short-term adaptation and an adaptation-independent surprise mechanism resisting anesthesia. In parallel, and only in wakefulness, VIP interneurons responded to the omission of the locally expected sound repeat at sequence ending, thus providing a chunking signal potentially useful for establishing global sequence structure. When this global structure was violated, by either shortening the sequence or ending it with a locally expected but globally unexpected sound transition, activity slightly increased in VIP and PV neurons respectively. Hence, distinct cellular mechanisms predict different regularity levels in sound sequences.</p>
Novel Asaia bogorensis signal sequences for Plasmodium inhibition in Anopheles stephensi
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Data from: Expressed vomeronasal type-1 receptors (V1rs) in bats uncover conserved sequences underlying social chemical signaling
In mammals, social and reproductive behaviors are mediated by chemical cues encoded by hyperdiverse families of receptors expressed in the vomeronasal organ. Between species, the number of intact receptors can vary by orders of magnitude. However, the evolutionary processes behind variation in receptor number, and its link to fitness-related behaviors are not well understood. From vomeronasal transcriptomes, we discovered the first evidence of intact vomeronasal type-1 receptor (V1r) genes in bats, and we tested whether putatively functional bat receptors were orthologous to those of related taxa, or whether bats have evolved novel receptors. Instead of lineage-specific duplications, we found that bat V1rs in bats show high levels of orthology to those of their relatives, and receptors are under comparative levels of purifying selection compared to non-bats. Despite widespread vomeronasal organ loss in bats, V1r copies have been retained for >65 million years. The highly conserved nature of bat V1rs challenges our current understanding of mammalian V1r function and suggest roles other than conspecific recognition or mating initiation in social behavior.
Decoding the pedogenic weathering signals from the red clay sequence on the Chinese Loess Plateau
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Nigrostriatal dopamine signals sequence-specific action-outcome prediction errors
<p>Data for Hollon et al. (2021) Nigrostriatal dopamine signals sequence-specific action-outcome prediction errors. <em>Current Biology</em></p>
Immunization of Patients With Metastatic Melanoma Using the GP100 Peptide Preceded by an Endoplasmic Reticulum Insertion Signal Sequence
ClinicalTrials.gov study NCT00001705. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Data from: Expressed vomeronasal type-1 receptors (V1rs) in bats uncover conserved sequences underlying social chemical signaling
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Data from: Breakdown of phylogenetic signal: a survey of microsatellite densities in 454 shotgun sequences from 154 non model eukaryote species
Microsatellites are ubiquitous in Eukaryotic genomes. A more complete understanding of their origin and spread can be gained from a comparison of their distribution within a phylogenetic context. Although information for model species is accumulating rapidly, it is insufficient due to a lack of species depth, thus intragroup variation is necessarily ignored. As such, apparent differences between groups may be overinflated and generalizations cannot be inferred until an analysis of the variation that exists within groups has been conducted. In this study, we examined microsatellite coverage and motif patterns from 454 shotgun sequences of 154 Eukaryote species from eight distantly related phyla (Cnidaria, Arthropoda, Onychophora, Bryozoa, Mollusca, Echinodermata, Chordata and Streptophyta) to test if a consistent phylogenetic pattern emerges from the microsatellite composition of these species. It is clear from our results that data from model species provide incomplete information regarding the existing microsatellite variability within the Eukaryotes. A very strong heterogeneity of microsatellite composition was found within most phyla, classes and even orders. Autocorrelation analyses indicated that while microsatellite contents of species within clades more recent than 200 Mya tend to be similar, the autocorrelation breaks down and becomes negative or non-significant with increasing divergence time. Therefore, the age of the taxon seems to be a primary factor in degrading the phylogenetic pattern present among related groups. The most recent classes or orders of Chordates still retain the pattern of their common ancestor. However, within older groups, such as classes of Arthropods, the phylogenetic pattern has been scrambled by the long independent evolution of the lineages.
Data from: GHOST: Recovering Historical Signal from Heterotachously-evolved Sequence Alignments
<p><span>Molecular sequence data that have evolved under the influence of heterotachous evolutionary processes are known to mislead phylogenetic inference. We introduce the General Heterogeneous evolution On a Single Topology (GHOST) model of sequence evolution, implemented under a maximum-likelihood framework in the phylogenetic program IQ-TREE (</span><a class="link link-uri" href="http://www.iqtree.org/">http://www.iqtree.org</a><span>). Simulations show that using the GHOST model, IQ-TREE can accurately recover the tree topology, branch lengths, and substitution model parameters from heterotachously evolved sequences. We investigate the performance of the GHOST model on empirical data by sampling phylogenomic alignments of varying lengths from a plastome alignment. We then carry out inference under the GHOST model on a phylogenomic data set composed of 248 genes from 16 taxa, where we find the GHOST model concurs with the currently accepted view, placing turtles as a sister lineage of archosaurs, in contrast to results obtained using traditional variable rates-across-sites models. Finally, we apply the model to a data set composed of a sodium channel gene of 11 fish taxa, finding that the GHOST model is able to elucidate a subtle component of the historical signal, linked to the previously established convergent evolution of the electric organ in two geographically distinct lineages of electric fish. We compare inference under the GHOST model to partitioning by codon position and show that, owing to the minimization of model constraints, the GHOST model offers unique biological insights when applied to empirical data.</span></p>
Nanopore signals corresponding to all negative sample sequences
<p>This dataset contains the nanopore signals of the negative samples in all datasets.</p>
Data from: Phylogenomics of phrynosomatid lizards: conflicting signals from sequence capture versus restriction site associated DNA sequencing
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Data from: Breakdown of phylogenetic signal: a survey of microsatellite densities in 454 shotgun sequences from 154 non model eukaryote species
Open the record for dataset details and reuse information.
Data from: GHOST: Recovering Historical Signal from Heterotachously-evolved Sequence Alignments
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Single-cell RNA sequencing reveals distinct transcriptional features of the purinergic signaling in mouse trigeminal ganglion
GEO Series GSE213105. Mus musculus. 1 samples. Type: Expression profiling by high throughput sequencing.
Next Generation Sequencing Facilitates Quantitative Analysis of germ cell RA signaling mutant and control THY1+ spermatogonia Transcriptomes
GEO Series GSE79863. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
Single-cell sequencing uncovers sensory neuron–mediated CGRP signaling as a driver of sarcoma progression
GEO Series GSE252589. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
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.