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3,109 results for “sequence analysis”
Fig 3 in Evolutionary relationships of Macaca fascicularis fascicularis (Raffles 1821) (Primates: Cercopithecidae) from Singapore revealed by Bayesian analysis of mitochondrial DNA sequences
Fig 3. Phylogenetic tree topology from Bayesian inference of 12S/tRNA-val/16S mtDNA sequences using a Birth-Death speciation tree prior, and HYK+G+I nucleotide substitution model in BEAST v2.1.3. Lettered identifications for clades are presented below the branches at major nodes. Posterior probabilities are displayed above the branches at nodes. Numbers in parentheses appearing with haplotype identifications are presented in Table 1, and correspond to numbered locations presented on the Figure 1 map. The Singapore haplotypes form two phylogenetic subgroupings, one from the Bukit Timah Nature Reserve (Sing1) and the other from the Central Catchment Nature Reserve (Sing2 & Sing3).
Fig 2 in Evolutionary relationships of Macaca fascicularis fascicularis (Raffles 1821) (Primates: Cercopithecidae) from Singapore revealed by Bayesian analysis of mitochondrial DNA sequences
Fig 2. Map of central Singapore showing the sampling locations in the Bukit Timah (BTNR) and Central Catchment (CCNR) Nature Reserves. Map created using ArcGIS® (ESRI® 2015).
Fig. 3. Sensitivity analysis graphic. Y in Total Evidence, Sequence Alignment, Evolution of Polychrotid Lizards, and a Reclassification of the Iguania (Squamata: Iguania)
Fig. 3. Sensitivity analysis graphic. Yaxis represents the logarithm of the ratio of transversion: transition weights. The xaxis represents the logarithm of the ratio of the indel cost versus the maximal cost of a molecular change. The colors represent the zaxis, which is congruence between the molecular and morphological data partitions. Red is good, blue is bad.
Fig. 1 in Populations analysis of the Brazilian Sharpnose Shark Rhizoprionodon lalandii (Chondrichthyes: Carcharhinidae) on the São Paulo coast, Southern Brazil: inferences from mt DNA sequences
Fig. 1. Median-joining haplotype network. The haplotypes are represented by circles, with the width proportional to their frequencies. Black circles correspond to Praia Grande, white to Ubatuba, and gray to Itanhaém samples. Each branch corresponds to a single mutation, except line a (with 2 mutations) and line b (with 3 mutations).
Data for: Human atlastin-3 is a constitutive ER membrane fusion catalyst (phylogenetic and sequence analysis)
<p>Homotypic membrane fusion catalyzed by the atlastin (ATL) GTPase sustains the branched endoplasmic reticulum (ER) network in metazoans. Our recent discovery that two of the three human ATL paralogs (ATL1/2) are C-terminally autoinhibited implied that relief of autoinhibition would be integral to the ATL fusion mechanism. An alternative hypothesis is that the third paralog ATL3 promotes constitutive ER fusion with relief of ATL1/2 autoinhibition used conditionally. However, published studies suggest ATL3 is a weak fusogen at best. Contrary to expectations, we demonstrate here that purified human ATL3 catalyzes efficient membrane fusion in vitro and is sufficient to sustain the ER network in triple knockout cells. Strikingly, ATL3 lacks any detectable C-terminal autoinhibition, like the invertebrate <em>Drosophila</em> ATL ortholog. Phylogenetic analysis of ATL C-termini indicates that C-terminal autoinhibition is a recent evolutionary innovation. We suggest that ATL3 is a constitutive ER fusion catalyst and that ATL1/2 autoinhibition likely evolved in vertebrates as a means of upregulating ER fusion activity on demand.</p>
Comparative Analysis of Droplet- vs. Microwell-based Whole Transcriptome Single-Cell Sequencing Technologies in Complex Human Tissues
<p>In the past decade, high-dimensional single-cell omics tools have enabled scientists to study the tumor microenvironment (TME) in unprecedented detail. However, recent investigations suggest that each technique has its unique strengths but also technology-inherent limitations. Here we directly compared two commercially available high-throughput single-cell RNA sequencing (scRNA-seq) technologies - droplet-based 10X Chromium <em>vs.</em> microwell-based BD Rhapsody - using paired samples from patients with localized prostate cancer (PCa) undergoing a radical prostatectomy.</p> <p>Although high technical consistency was observed in unraveling the whole transcriptome, the relative abundance of detectable cell populations differed. This could in part be ascribed to differences in the performance to recover cells with low-mRNA content. Hence, immune cells such as neutrophils are underrepresented in data generated with the widely used droplet-based scRNA-seq protocol, highlighting the importance of considering platform limitations in low mRNA content cell recovery. In contrast, droplet-based scRNA-seq demonstrated superiority in terms of recovering cells of epithelial origin. Moreover, we discovered platform-dependent variabilities in mRNA quantification and cell-type marker annotation, affecting the composition of identified tissue profiles and the exploratory value of the generated datasets. Overall, our study emphasizes the importance of carefully selecting the appropriate scRNA-seq platform to improve cell type representation and obtain a more comprehensive and accurate understanding of the TME.</p>
Model-based analysis of sample index hopping reveals its widespread artifacts in multiplexed single-cell RNA-sequencing
<p>Supplementary data that are needed to rerun the reproducible notebooks from the first steps using Alevin output and configuration files.</p> <p>Intermediate R data object that can be used to rerun the reproducible notebooks after the filtering steps.</p> <p>Validation data for inferring the sample index hopping rate. The <em>hiseq4000_joined_datatable_plexed_nonplexed.zip file contains read counts for four samples (two non-multiplexed and two multiplexed) joined by a cell-barcode, UMI, and gene-ID (CUG) key combination. The hiseq4000_inner_joined_with_labels.zip file contains only those CUGs that are observed in both the non-multiplexed and multiplexed samples.</em><em> </em></p>
Genome sequencing of three Orestias species and the analysis of their phylogenetic relationships within the Cyprinodontiformes order
<p>Relevant files and datasets for the paper: <em>"Genomes of the Orestias pupfish from the Andean Altiplano shed light on their evolutionary history and phylogenetic relationships within Cyprinodontiformes." </em>by Morales <em>et al</em>.</p>
Data for: Range and niche expansion through multiple interspecific hybridization - a genotyping by sequencing analysis of Cherleria (Caryophyllaceae)
Open the record for dataset details and reuse information.
Joint analysis of microsatellites and flanking sequences enlightens complex demographic history of interspecific gene flow and vicariance in rear-edge oak populations
Open the record for dataset details and reuse information.
Data for: Human atlastin-3 is a constitutive ER membrane fusion catalyst (phylogenetic and sequence analysis)
Open the record for dataset details and reuse information.
Sequence data from viral assembly graph analysis of the SERC virome
<p>Various sequence data and details that were used in publishing the manuscript describing assembly graph binning in the SERC viral metagenome. Including: assembled contigs, FASTG, predicted ORFs, two tables describing the assembled contigs and graphs.</p> <p>Also PolA and RNR sequences that were mined from the SERC assembly.</p>
A Bayesian Phylogenetic Hidden Markov Model for B Cell Receptor Sequence Analysis
<p>simulation and PC64/VRC01 input/output data files</p>
Dataset used for "Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data"
<p>Each simulated dataset was generated using the AbSim R package (version 0.2.6) in a B cell single-lineage fashion. Each B cell clone simulation begins with a random selection from sets of IGHV, IGHD, and IGHJ germline sequences to produce a unique V(D)J recombination event. Then, clones are made by introducing mutations using a local nucleotide context-dependent model (S5F model) along a phylogenetic tree in which branching events occur stochastically. </p>
Fluorescent (C)LSM image sequences of Dictyostelium discoideum (Ax2 - LifeAct mRFP) for cell track and cell contour analysis
<p>This data set is designed for cell contour and cell track analysis. Hence image sequences of moving Dictyostelium discoideum cells are recorded. For the purpose to facilitate the detection of the cell contour we take fluorescent images of the cortical protein actin to obtain a high contrast between background and cell body. In each image sequences several cells are recorded. This allows for an analysis of all cells at once or to crop single cell tracks.</p>
Homology analysis of HCV sequences obtained from a dialysis unit of northeast India
<p>This is a homology analysis (by DNASTAR MegaAlign Version 5.00) of 29 HCV Sequences (5'UTR-Core region sequencing) obtained from a dialysis unit of a tertiary care teaching hospital in northeast India. It is a part of a manuscript titled- "Circulation of an atypical hepatitis C virus (HCV) strain in a dialysis unit in northeast India". </p>
Supplementary table with homology analysis of twenty nine HCV sequences ((5'UTR-Core region) )
<p>It is a supplementary data table with homology analysis of 29 HCV sequences ((5’UTR-Core region) obtained from a dialysis unit of a tertiary care teaching hospital of Northeast India (Assam). It is a part (supplementary data) of the manuscript titled - "Circulation of an atypical hepatitis C virus (HCV) strain in a dialysis unit in northeast India" </p>
Sequence data for the article "Whole transcriptome analysis of thousands of FACS-sorted single cells with the single cell nanoCAGE protocol" - single cells dataset
<p>Sequence data (Illumina MiSeq runs) for the article "Whole transcriptome analysis of thousands of FACS-sorted single cells with the single cell nanoCAGE protocol". dataset of 2300 single cells. File names indicate unique sequencing runs. In the manuscripts, the informations about cell lines are found in the Supplemental Table 1. </p>
Sequence data for the article "Whole transcriptome analysis of thousands of FACS-sorted single cells with the single cell nanoCAGE protocol" - Protocol optimization
<p>Sequence data (Illumina MiSeq runs) for the article "Whole transcriptome analysis of thousands of FACS-sorted single cells with the single cell nanoCAGE protocol". Optimization of the protocol. Files names indicate unique run identifiers. In the manuscript, the link between unique run identifiers, cells and purpose of the experiment is found in the Supplemental Table 1. </p>
Multimodal Epigenetic Sequencing Analysis (MESA) of Cell-free DNA for Non-invasive Colorectal Cancer Detection
<p>Processed data (feature-by-sample matrices) of non-disruptive bisulfite-free methylation sequencing for cfDNA samples from 4 clinical cohorts (Cohort 1, Cohort 2, Cohort 3, and cfTAPS dataset). Codes used to repeat the results in our paper can be found https://rpubs.com/LiYumei/926228 and https://github.com/ChaorongC/MESA. </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.