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1,297 results for “differential analysis”
Fig. 2 in Differentiation of Trichuris species eggs from non-human primates by geometric morphometric analysis
Fig. 2. Trichuris sp. egg lineal measurements. L1: maximum width of polar opercula, L2: minimum width of polar opercula, L3: base width of polar opercula, L4: length of polar opercula, measured from exterior midpoint to the narrow midpoint, L5: total length of polar opercula, measured from the exterior midpoint to the base midpoint, L6: wall thickness at its midpoint, L7: wall thickness in contact with polar opercula, L8: interior length of the egg.
Fig. 3. A in Differential proteomic analysis of date palm leaves infested with the red palm weevil (Coleoptera: Curculionidae)
Fig. 3. A pie chart presenting the classification of identified proteins according to their biological functions, expressed in percentage.
Fig. 1 in Differential proteomic analysis of date palm leaves infested with the red palm weevil (Coleoptera: Curculionidae)
Fig. 1. Two-dimensional differential gel electrophoresis representative images of date palm proteins. The protein sample of control, wounded, infested, and internal standard (pooled of all the samples) are individually labeled with Cy dyes, mixed together and separated by two-dimensional differential gel electrophoresis followed by image scanning. (A) image of date palm control sample and labeled with cy3 dye; (B) image of date palm artificially wounded sample labeled with cy5 dye; (C) image of date palm sample infested with red palm weevil and labeled with cy3 dye; (D) image of date palm sample pooled from all and labeled with cy2 dye; (E) overlay gel of control, infested, and wounded along with internal standard.
Fig. 2 in Differential proteomic analysis of date palm leaves infested with the red palm weevil (Coleoptera: Curculionidae)
Fig. 2. Venn diagram for the relative distribution of proteins spots in control, mechanically wounded, and red palm weevil infested date palm samples. The non-overlapping segment of diagram represent the number of proteins which were significantly up-regulated (> 1.5-fold) in the corresponding group when compared with the other two groups. The overlapping region between any two groups represents the number of protein spots significantly up-regulated (> 1.5-fold) compared to the third one. The central overlapping region depicts the protein spots where no statistically significant change in up- or down-regulation was observed.
Hepatic transcriptomic analysis reveals differential regulation of metabolic and immune pathways in three strains of chickens with distinct growth rate exposed to mixed parasites infections
<p><span>This dataset was generated from the study investigating hepatic gene expression in three strains of chickens: Ross-308 (R), Lohmann Brown Plus (LB), and Lohmann Dual (LD), 2 weeks after either an experimental infection (n = 18) with both <em>A. galli</em> and <em>H. gallinarum or kept as uninfected control (n = 12)</em>. </span></p>
Acid fractionation during carbonate digestion with phosphoric acid – Assessment of two different techniques applied for clumped and stable isotope analysis using a Tuneable Infrared Laser Differential Absorption Spectrometer (TILDAS) [dataset]
<p>Date files : </p> <table> <tbody> <tr> <td> <p>Data 1 (Relationship between Mixing ratio difference of sample and WRG and D638 value).xlsx;Data 2 (Role of bulk isotope composition (δ628 & δ636) on Δ638).xlsx;Data 3 (CDES scale conversion).xlsx;Data 4 (VPDB scale conversion for d628 and d636).xlsx;Data 5 (Reference material values).xlsx;Data 6 (Break seal method acid fractionation factor of calcite).xlsx;Data 7 (IAB method acid fractionation factor of calcite).xlsx</p> </td> </tr> </tbody> </table>
Extended data tables to Haering and Habermann, F1000Res, RNfuzzyApp: an R shiny RNA-seq data analysis app for visualisation, differential expression analysis, time-series clustering and enrichment analysis
<p><b>Background</b> </p> <p>RNA-seq is a widely adopted affordable method for large scale gene expression profiling. However, user-friendly and versatile tools for wet-lab biologists to analyse RNA-seq data beyond standard analyses such as differential expression, are rare. Especially, the analysis of time-series data is difficult for wet-lab biologists lacking advanced computational training. Furthermore, most meta-analysis tools are tailored for model organisms and not easily adaptable to other species.</p> <p><b>Results</b></p> <p>With RNfuzzyApp, we provide a user-friendly, web-based R-shiny app for differential expression analysis, as well as time-series analysis of RNA-seq data. RNfuzzyApp offers several methods for normalization and differential expression analysis of RNA-seq data, providing easy-to-use toolboxes, interactive plots and downloadable results. For time-series analysis, RNfuzzyApp presents the first web-based, automated pipeline for soft clustering with the Mfuzz R package, including methods to aid in cluster number selection, Mfuzz loop computations, cluster overlap analysis, as well as cluster enrichments.</p> <p><b>Conclusion</b></p> <p>RNfuzzyApp is an intuitive, easy to use and interactive R shiny app for RNA-seq differential expression and time-series analysis, offering a rich selection of interactive plots, providing a quick overview of raw data and generating rapid analysis results. Furthermore, its orthology assignment, enrichment analysis, as well as ID conversion functions are accessible to non-model organisms.</p>
Simulation data for "Phylogenetic analysis of migration, differentiation, and class switching in B cells"
<p>Simulation data for https://doi.org/10.1101/2020.05.30.124446.</p> <p>Scripts available at: https://bitbucket.org/kleinstein/projects/src/master/Hoehn2020/</p> <p>data_twostate.tsv: AIRR TSV file of data used for simulations</p> <p>trees_twostate.RData: Tree topologies used to simulate migration</p> <p>simulations.tar.gz: Files used in simulation analyses. File names show:</p> <p><rate (r)>_<rate A to B (r_ab)>_<pi_A>_<repetition></p> <p>laddersims.tar.gz: Files used in ladder tree simulation analyses. File names show:</p> <p><rate (r)>_<rate A to B (r_ab)>_<pi_A>_<number of tips>_<number of trees>_<repetition></p> <p> </p>
Text-fig. 28. Scanning electron microscope (SEM) images of monocolpate pollen of Goczania inaequalis sp. nov.; Torres Vedras locality, Portugal. a) Holotype; stamen fragment that yielded the pollen in (b–f, k); b) Group of pollen grains showing distal and proximal surfaces and inner surface of anther wall with densely spaced orbicules; c) Inner surface of anther wall showing small, spherical orbicules with microechinate sculpturing; d, e, j–l) Pollen grains in distal and equatorial view (k) showing the long colpus with an irregular margin flanked by narrow bands of poorly differentiated microechinate; note that colpus is aligned perpendicular to the longest axes in elliptical grains and that the pollen wall is almost psilate around the equator and in the distal in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 28. Scanning electron microscope (SEM) images of monocolpate pollen of Goczania inaequalis sp. nov.; Torres Vedras locality, Portugal. a) Holotype; stamen fragment that yielded the pollen in (b–f, k); b) Group of pollen grains showing distal and proximal surfaces and inner surface of anther wall with densely spaced orbicules; c) Inner surface of anther wall showing small, spherical orbicules with microechinate sculpturing; d, e, j–l) Pollen grains in distal and equatorial view (k) showing the long colpus with an irregular margin flanked by narrow bands of poorly differentiated microechinate; note that colpus is aligned perpendicular to the longest axes in elliptical grains and that the pollen wall is almost psilate around the equator and in the distal
Text-fig. 29. Scanning electron microscope (SEM) images of monocolpate pollen of Goczania punctata sp. nov.; Torres Vedras locality, Portugal. a–c) Holotype; anther fragment (a) with group of pollen grains showing the distal face (b, c) with clearly delimited colpus, the almost psilate tectum with occasional small perforations, and poorly differentiated microechinae on the proximal face (b). Specimen, TV44-S148024 (holotype). Scale bars 300 Μm (a), 6 Μm (b, c). in The Early Cretaceous Mesofossil Flora Of Torres Vedras (Ne Of Forte Da Forca), Portugal: A Palaeofloristic Analysis Of An Early Angiosperm Community
Text-fig. 29. Scanning electron microscope (SEM) images of monocolpate pollen of Goczania punctata sp. nov.; Torres Vedras locality, Portugal. a–c) Holotype; anther fragment (a) with group of pollen grains showing the distal face (b, c) with clearly delimited colpus, the almost psilate tectum with occasional small perforations, and poorly differentiated microechinae on the proximal face (b). Specimen, TV44-S148024 (holotype). Scale bars 300 Μm (a), 6 Μm (b, c).
Data from: Potentials of closed contour analysis in species differentiation and holotype designation: a case study on lower Norian (Upper Triassic) conodonts
<p><span>Geometric morphometric approaches become increasingly applied in the fields of biology and paleontology. Taxonomy is a good example, where a long-standing intention of scientists is to eliminate subjectivity as much as possible. In the case of biostratigraphically important conodont elements, the application of such methods is not widespread. Indeed, only a handful of studies attempted to deal with the morphological variance of conodont elements from this aspect. The detailed description of five lower Norian (Upper Triassic) taxa (<em>Ancyrogondolella quadrata, A. rigoi, A. triangularis, A. uniformis</em> and <em>Metapolygnathus mazzai</em>) is presented here based on landmarks and Fourier analysis of the P1 element and keel outlines. Both methods led to similar outcomes regarding taxonomic differentiation and exposing shape variability. Consensus shapes were generated to objectively reveal the typical contour shape of each taxon, which allowed their comparison with each other, and with the members of their respective sample population including the holotypes. The results pointed out that the holotype of a taxon is generally not an average representative, but rather a peripheral form with well-separable morphological characteristics. <em>Ancyrogondolella quadrata</em> and <em>A. rigoi</em> turned out to represent a morphological continuum with ample transitional forms between these two end-members that may cause bias in their biostratigraphic applicability; however, their combined shape variance seems to be too large for uniting them into a single species. Given the results that may be too subtle to realize based solely on qualitative observations, future taxonomic studies and type material designation could greatly benefit from the application of similar methodologies.</span></p>
RNAseq data: Analysis of circRNA expression in human neuronal differentiation
<p>This dataset contains sequencing read count data related to samples from differentiating human neuroepithelial stem cells (NES) collected at days zero (NES), five (D5) and 28 (D28) of differentiation. Details on how samples were collected and how data was generated and processed are described below.</p> <p> </p> <p><em>Sample preparation</em></p> <p>NES were seeded on tissue culture flasks coated with 20 μg/ml poly-L-ornithine (Sigma-Aldrich P3655), and 1 μg/ml laminin (Sigma-Aldrich L2020). Cells were grown in DMEM/F12+GlutaMAX medium (ThermoFisher 31331093) supplemented with 0.05X B27 (ThermoFisher 17504044), 1X N2 (ThermoFisher 17502001), 10 ng/ml bFGF (fisher scientific CTP0261), 10 ng/ml EGF (PeproTech AF-100-15) and 10 U/ml penicillin/streptomycin (ThermoFisher 15140122). Medium was exchanged 50% daily and cells maintained in 5% CO2 at 37ºC, passaging once 100% confluent and seeding at a density of 5x104 cells/cm2. Neural differentiation was induced by growth factor withdrawal the day after plating with media B27 concentration increased to 0.5X. Media was exchanged 50% every second day up until D15, after which media was supplemented with 0.4 ug/ml laminin and exchanged 50% every three days. </p> <p> </p> <p><em>RNA extraction and sequencing</em></p> <p>Cells were lysed in TRIzol reagent (ThermoFischer 15596026) before separating with chloroform and mixing the aqueous phase with isopropanol as per manufacturer directions. RNA was then isolated from the isopropanol/chloroform solution using the ReliaPrep RNA Cell Miniprep kit (Promega Z6010). Libraries were prepared with Illumina Truseq Stranded total RNA RiboZero GOLD kit and sequenced on the NovaSeq6000 platform with a 2x151 setup using NovaSeqXp workflow in S4 mode flowcell.</p> <p> </p> <p><em>Data generation</em></p> <p>Raw reads were processed using cutadapt v3.2 to trim adaptor sequences and low-quality base pairs and discard short reads (options: -m 20 -e 0.1 -q 20 -O 1). The GRCh37 genome assembly was used for all alignment, annotation, and downstream analysis steps. Trimmed read weres alignment to the GRCh37 genome assembly using TopHat v2.0.9 tophat_fusion (with Bowtie v1.1.2 and Samtools v0.1.19) with –fusion-min-dist 200. BAM files have been anonymised by removal of potentially identifiable genetic variant information using BAMboozle v0.5.0 (Ziegenhain & Sandberg, 2021) with default settings. This BAM files and corresponding index (.bai) files are provided here with naming convention "<em>label.</em>bam" Information on sample labels and corresponding conditions is provided in the file 'metadata.txt'.</p> <p><br> </p>
Results of the differential gene expression analysis in SIV infection in Chlorocebus sabaeus and Macaca mulatta
<p>Results of differential gene expression analysis in SIV infection in Chlorocebus sabaeus and Macaca mulatta.</p> <p>From the transcriptome data repository MACE (http://mace.ihes.fr)</p>
The raw microarray data and the differential expression analysis results from "Manipulating the growth environment through co-culture to enhance stress tolerance and viability of probiotic strains in the gastrointestinal tract".
<p>The signal data for each spot were subsequently quantified by using Feature Extraction software (Agilent Technologies).M1.txt to M5.txt: monoculture; C1.txt to C5.txt: co-culture; P1.txt to P5.txt: pH-controlled monoculture. The differential expression analysis results were obtained by using limma.</p>
Extended data tables to Haering and Habermann, F1000Res, RNfuzzyApp: an R shiny RNA-seq data analysis app for visualisation, differential expression analysis, time-series clustering and enrichment analysis
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Data from: Potentials of closed contour analysis in species differentiation and holotype designation: a case study on lower Norian (Upper Triassic) conodonts
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Replicated differential expression analysis in a green-brown polymorphic grasshopper reveals role of beta-carotene-binding protein in body coloration
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Refining impact assessment in undergraduate STEM education: Differential item functioning analysis of field-based learning interventions
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Two-step mixed model approach to analyzing differential alternative RNA splicing: Datasets and R scripts for analysis of alternative splicing
<p>Changes in gene expression can correlate with poor disease outcomes in two ways: through changes in relative transcript levels or through alternative RNA splicing leading to changes in relative abundance of individual transcript isoforms. The objective of this research is to develop new statistical methods in detecting and analyzing both differentially expressed and spliced isoforms, which appropriately account for the dependence between isoforms and multiple testing corrections for the multi-dimensional structure of at both the gene- and isoform- level. We developed a linear mixed effects model-based approach for analyzing the complex alternative RNA splicing regulation patterns detected by whole-transcriptome RNA-sequencing technologies. This approach thoroughly characterizes and differentiates three types of genes related to alternative RNA splicing events with distinct differential expression/splicing patterns. We applied the concept of appropriately controlling for the gene-level overall false discovery rate (OFDR) in this multi-dimensional alternative RNA splicing analysis utilizing a two-step hierarchical hypothesis testing framework. In the initial screening test we identify genes that have differentially expressed or spliced isoforms; in the subsequent confirmatory testing stage we examine only the isoforms for genes that have passed the screening tests. Comparisons with other methods through application to a whole transcriptome RNA-Seq study of adenoid cystic carcinoma and extensive simulation studies have demonstrated the advantages and improved performances of our method. Our proposed method appropriately controls the gene-level OFDR, maintains statistical power, and is flexible to incorporate advanced experimental designs.</p>
Data from: Spider webs, stable isotopes and molecular gut content analysis: multiple lines of evidence support trophic niche differentiation in a community of Hawaiian spiders
1. Adaptive radiations are typically characterized by niche partitioning among their constituent species. Trophic niche partitioning is particularly important in predatory animals, which rely on limited food resources for survival. 2. We test for trophic niche partitioning in an adaptive radiation of Hawaiian Tetragnatha spiders, which have diversified in situ on the Hawaiian Islands. We focus on a community of nine species belonging to two different clades, one web building and the other actively hunting, which co-occur in wet forest on East Maui. We hypothesize that trophic niches differ significantly both 1) among species within a clade, indicating food resource partitioning, and 2) between the two clades, corresponding with their differences in foraging strategy. 3. To assess niches of the spider species, we measure a) web architecture, the structure of the hunting tool, and b) site choice, the physical placement of the web in the habitat. We then test whether differences in these parameters translate into meaningful differences in trophic niche by measuring c) stable isotope signatures of carbon and nitrogen in the spiders' tissues, and d) gut content of spiders based on metabarcoding data. 4. We find significant interspecific differences in web architecture and site choice. Importantly, these differences are reflected in stable isotope signatures among the five web-building species, as well as significant isotopic differences between web-builders and active hunters. Gut content data also show interspecific and inter-clade differences. Pairwise overlaps of web architecture between species are positively correlated with overlaps of isotopic signature. 5. Our results reveal trophic niche partitioning among species within each clade, as well as between the web-building and actively hunting clades. Based on the correlation between web architecture and stable isotopes, it appears that the isotopic signatures of spiders' tissues are influenced by architectural differences among their webs. Our findings indicate an important link between web structure, microhabitat preference and diet in the Hawaiian Tetragnatha.
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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.