Data from: Trade-offs drive resource specialization and the gradual establishment of ecotypesBjørn Østman, Randall Lin & Christoph Adami
Background: Speciation is driven by many different factors. Among those are trade-offs between different ways an organism utilizes resources, and these trade-offs can constrain the manner in which selection can optimize traits. Limited migration among allopatric populations and species interactions can also drive speciation, but here we ask if trade-offs alone are sufficient to drive speciation in the absence of other factors. Results: We present a model to study the effects of trade-offs on specialization...
Ben-David et al 2021 scRNAseq dataset wrangled into standard WormBase anndata- 55k cells profiled with 10xv2 at L2 larval stageEduardo da Veiga Beltrame
This is part of a curated collection of all C. elegans single cell RNA sequencing high throughput data wrangled into the anndata format in .h5ad files with standard fields, plus any number of optional fields that vary depending on the metadata the authors provide. As possible, we attempt to keep the field names lower case, short, descriptive, and only using valid Python variable names so they may be accessed via the syntax adata.var.field_name For the...
Earthquake Waveforms from Curvelet-denoising Paper (Data Supplement)
These are MAT files of the earthquake waveforms used to create figures in the paper "A unified wavefield-partitioning approach for distributed acoustic sensing."
SUGARseq_TMG_Opt_cDNA_FASTQJohn W. Thompson Katsuya L. Colon
FASTQ files for transcriptome
Alternative figures for \"Xylem hydraulic safety and efficiency tradeoff is impacted by its coupling to stomatal control\"Yujie Wang
File description: figs_s1.zip: Examples of photosynthetic rate, loss of plant hydraulic conductance, soil water content, accumulated water use efficiency, and growing season mean photosynthetic rate for 20 sites and 6 years (120 figures in total). figs_s2.zip: Examples of photosynthetic rate and loss of plant hydraulic conductance contours for 20 sites at year 2005 (20 figures in total). figs_s3.zip: Inter-annual variations in optimum hydraulic safety and efficiency combinations for 20 sites and 6 years (20 figures...
Tracing Carbonate Formation, Serpentinization, and Biological Materials with Micro-/Meso-Scale Infrared Imaging Spectroscopy in a Mars Analog System, Samail Ophiolite, OmanEllen K. Leask, Bethany L. Ehlmann, Rebecca N. Greenberger, Patrick Pinet, Yves Daydou, Georges Ceuleneer & Peter Kelemen
This dataset underlies the following publication, which must be cited with use of the dataset: Leask, E. K., B. L. Ehlmann, R. N. Greenberger, P. Pinet, Y. Daydou, G. Ceuleneer, and P. Kelemen (accepted), Tracing carbonate formation, serpentinization, and biological materials with micro-/meso-scale infrared imaging spectroscopy in a Mars analog system, Samail ophiolite, Oman, Earth and Space Science. Data used in each figure or analysis presented in the paper are archived here. Data are atmospherically...
The Mouse Action Recognition System (MARS): behavior annotation dataCristina Segalin, Jalani Williams, Tomomi Karigo, May Hui, Moriel Zelikowski, Jennifer J. Sun, Pietro Perona, David J. Anderson & Ann Kennedy
The study of naturalistic social behavior requires quantification of animals' interactions. This is generally done through manual annotation—a highly time consuming and tedious process. Recent advances in computer vision enable tracking the pose (posture) of freely-behaving animals. However, automatically and accurately classifying complex social behaviors remains technically challenging. We recently introduced the Mouse Action Recognition System (MARS), an automated pipeline for pose estimation and behavior quantification in pairs of freely interacting mice (Segalin et al,...
bi183 VMH metadataTara Chari
Cell Metadata csv for 10x VMH neurons from Kim et al. 2019
Quantitative sequencing clarifies the role of disruptor taxa, the oral microbiome, and strict anaerobes in the human small-intestine microbiomeJacob Barlow, Gabriela Leite, Anna Romano, Ali Rezaie, Ruchi Mathur, Mark Pimentel, Rustem Ismagilov, , &
Raw data and processing scripts for manuscript. All processing scripts are python jupyter notebooks. Unzip data file folders and keep the folder hierarchy as is or alter path locations in jupyter notebooks.
Code and Data for 'Unearthing real time 3D ant tunneling mechanics', , , , , &
All code and data for the paper 'Unearthing real time 3D ant tunneling mechanics', submitted to PNAS
d13C and d34S of Dissolved Organic Matter (DOM, DOS)Alexandra Phillips
Data set of SPE extracted Dissolved Organic Matter samples that accompanies A Phillips' Thesis Chapter 3 on resolving sources of DOM using novel sulfur isotope analysis. Contains relevant metadata as well as measured parameters (d13C, d34S, C/S)
CeNGEN scRNAseq dataset wrangled into standard WormBase anndata - 100k C. elegans cells FACS sorted for neurons in L4 larvaeEduardo da Veiga Beltrame
CeNGEN (Taylor et al 2021) scRNAseq dataset wrangled into standard WormBase anndata 100k C. elegans cells FACS sorted to enrich for neurons - 70k cells are neurons, 30k are other types For more information about the data see the CeNGEN project website: https://cengen.org Preprint describing data and analysises: https://doi.org/10.1101/2020.12.15.422897 Molecular topography of an entire nervous system - bioRxiv 2020 Seth R Taylor, Gabriel Santpere, Alexis Weinreb, Alec Barrett, Molly B. Reilly, Chuan Xu, Erdem Varol,...
Distributed acoustic sensing recorded Ridgecrest Earthquake aftershocksJames Atterholt
This data set is composed of 30-second time windows that encompass the early onset waveforms of 50 high SNR earthquakes recorded by a distributed acoustic sensing array in Ridgecrest, CA
10 scRNA-seq datasets processed using 3 unspliced counting pipelinesGennady Gorin & Tara Chari
This dataset contains ten 10X scRNA-seq datasets (two v2 from Desai et al., DOI: 10.1126/science.abc6506, eight v3 generated by 10X Genomics) that have been processed using pipelines for spliced and unspliced molecule quantification. We used velocyto, kallisto|bustools (kb), and salmon/alevin-fry to process the raw FASTQ files, and output loompy files with spliced and unspliced count matrices. The scripts used for processing, as well as the notebook used for post-processing, visualization, and comparisons are available at...
Regeneration data - JellyfishMichael Abrams, Ty Basinger & Lea Goentoro
Abrams et al., 2020 (doi: https://doi.org/10.1101/2020.11.21.392720). This dataset contains the raw images analyzed and quantified for generating Figure 3 and the associated supplementary figures. The czi files can be opened and analyzed using the Zeiss Zen software or the freeware Fiji. All images were taken at the same magnification. See the manuscript for more technical details.
Specious Art Pseudotime Lineage Cell Metadata
Cell metadata csv for Packer and Zhu et al dataset used for pseudotime analysis
Specious Art Pseudotime Lineage Gene MetadataTara Chari
Gene metadata Packer and Zhu et al dataset, for pseudotime analysis
Code for Crystal Knob xenoliths projectDaven P. Quinn
Code repository for creating the analytical results of the Crystal Knob xenolith project.
Flow Cytometry CSV Files for \"An allosteric theory of transcription factor induction.\", , , , &
These data correspond to the comma separated value files converted from the original flow cytometry standard (.fcs) files generated from the experimental measurement of fluorescence on a MiltenyiBiotec MACSQuant flow cytometer. These files were passed through a processing pipeline to quantify the fold-change in gene expression due to action by the Lac repressor. These data are separated by the operator we examined. Eight different strains were measured for each dataset. Please see the main text...
Data from: The function and organization of the motor system controlling flight maneuvers in fliesTheodore H. Lindsay, Anne Sustar, Michael H. Dickinson, Theodore Lindsay & Michael Dickinson
Animals face the daunting task of controlling their limbs using a small set of highly constrained actuators. This problem is particularly demanding for insects such as Drosophila, which must adjust wing motion for both quick voluntary maneuvers and slow compensatory reflexes using only a dozen pairs of muscles. To identify strategies by which animals execute precise actions using sparse motor networks, we imaged the activity of a complete ensemble of wing control muscles in intact,...
Data from: A descending neuron correlated with the rapid steering maneuvers of flying DrosophilaBettina Schnell, Ivo G. Ros & Michael H. Dickinson
To navigate through the world, animals must stabilize their path against disturbances and change direction to avoid obstacles and to search for resources. Locomotion is thus guided by sensory cues but also depends on intrinsic processes, such as motivation and physiological state. Flies, for example, turn with the direction of large-field rotatory motion, an optomotor reflex that is thought to help them fly straight. Occasionally, however, they execute fast turns, called body saccades, either spontaneously...
Data from: On the convergence and accuracy of the cardiovascular intrinsic frequency methodPeyman Tavallali, Thomas Y. Hou, Derek G. Rinderknecht & Niema M. Pahlevan
In this paper, we analyse the convergence, accuracy and stability of the intrinsic frequency (IF) method. The IF method is a descendant of the sparse time frequency representation methods. These methods are designed for analysing nonlinear and non-stationary signals. Specifically, the IF method is created to address the cardiovascular system that by nature is a nonlinear and non-stationary dynamical system. The IF method is capable of handling specific nonlinear and non-stationary signals with less mathematical...
AAV-PHP.S transduction across multiple layers of the small intestineKen Chan & Viviana Gradinaru
A video demonstrating the transduction of AAV-PHP.S across multiple layers of the small intestine after optical clearing with refractive index matching solution (RIMS). Native GFP fluorescence (green) from ssAAV-PHP.S:CAG-NLS-GFP at 1 x 1012vg/mouse is shown. S100b staining (magenta) is shown for contrast.
X-ray Diffraction of Cu-Ca-V oxidesJohn Gregoire & Lan Zhou
Series of XRD patterns collected on a Bruker D8 system using a composition library made by sputter deposition. File format consistent with that described at udiscover.it.
Simulated radiance and retrieved variables (XCO2 and SIF) for the Orbiting Carbon Observatory-3 (OCO-3) MissionAnnmarie Eldering
This is a pre-launch simulated dataset for OCO-3 (Orbiting Carbon Observatory-3). Simulated satellite measurements from the ISS include the radiances observed in 3 bands (~765nm, 1.6 microns, and 2.1 microns) are provided along with the results from two cloud screening algorithms. The L2 retrievals of carbon dioxide dry air mole fraction (XCO2) and solar induced fluorescence (SIF) are included. The meteorology and surface properties used in the simulation are also archived.
California Institute of Technology27,055
California Institute of Technology, Pasadena, CA (US)29
Jet Propulsion Lab26
United States National Library of Medicine8
University of Washington7
Huazhong University of Science and Technology6
Shanghai University of Traditional Chinese Medicine6