Data and analysis notebook for single cell studies database manuscript
This deposit contains a snapshot of data, and a Jupyter notebook that was used to generate figures from the data, which serves as an example for how the data can be investigated
Ensemble model output of North American atmospheric CO2 simulation (full WRF-chem output)S. Feng, T. Lauvaux, K.J. Davis, K. Keller, R. Rayner, T. Oda, K. Gurney, Y. Zhou, C. Williams, A.E. Schuh, J. Liu & I. Baker
The uncertainty in biospheric carbon dioxide (CO2) flux estimates drives divergent projections of future climate and uncertainty in prescriptions for climate mitigation. The terrestrial carbon sink can be inferred from atmospheric CO2 observations with transport models via inversion methods. Regional CO2 flux estimates remain uncertain due to the mixture of uncertainties caused by transport models, prior estimates of biospheric fluxes, large-scale CO2 boundary inflow, the assumptions in the inversion process, and the limited density of...
Experimental velocity measurements of sub-Rayleigh and superstar rupturesVito Rubino, Ares Rosakis & Nadia Lapusta
The experimental velocity measurements of sub-Rayleigh and superstar ruptures are provided for the four experiments discussed in the related publication. Variable names used in the MAT files are explained in the "Readme" file.
Supplementary data tables for Composition, Stratigraphy, and Geological History of the Noachian Basement Surrounding the Isidis Impact Basin&
Three supplementary data tables: Supplement 1 contains the texture and HiRISE color properties evaluated for all mapped megabreccia outcrops. Megabreccia outcrop positions are given as X,Y,elevation-locations in the global MOLA mosaic with projection of SimpleCylindrical_Mars. Supplement 2 contains all measured megabreccia block sizes and their locations in the same format as supplement 1. Supplement 3 contains all orientation measurements (strike, dip, and rake errors) from layers and contact segments of Stratified Basement within 2 different...
Downscaled 500-m TROPOMI SIF over CaliforniaChristian Frankenberg
Data is saved as self-contained daily netCDF4 files -------------------------------------------------------------------- USE OF DOWNSCALED TROPOMI SIF DATA These data are made freely available to the public and the scientific community in the belief that their wide dissemination will lead to greater understanding and new scientific insights. The availability of these data does not constitute publication of the data. We rely on the ethics and integrity of the user to receive fair credit for our work. If the...
Processed Images and Summary Files for \"Phsyiological Adaptability and Parametric Versatility in a Simple Genetic Circuit\"Griffin Chure, Zofii A. Kaczmarek & Rob Phillips
This data set contains Matlab `clist` files that are derived from segmentation and lineage tracking of bacterial cells growing under a microscope. This data set can be used to extract information about segmented cells, but contains no images.
Self-reinoculation with fecal flora changes microbiota density and composition leading to an altered bile-acid profile in the mouse small intestineSaid R. Bogatyrev, Justin C. Rolando & Rustem F. Ismagilov
Background: The upper gastrointestinal tract plays a prominent role in human physiology as the primary site for enzymatic digestion and nutrient absorption, immune sampling, and drug uptake. Alterations to the small-intestine microbiome have been implicated in various human diseases, such as non-alcoholic steatohepatitis and inflammatory bowel conditions. Yet, the physiological and functional roles of the small-intestine microbiota in humans remain poorly characterized because of the complexities associated with its sampling. Rodent models are used extensively...
Cell intensities extracted from microscopy images for \"First-principles prediction of the information processing capacity of a simple genetic circuit.\"Manuel Razo-Mejia, Rob Phillips, Sarah Marzen, Griffin Chure, Rachel Taubman & Muir Morrison
These data correspond to the single-cell mean intensity values obtained from microscopy images used to quantify fluorescence and compute gene expression distributions due to the activity of the Lac repressor molecule in E. coli cells. This information was used to compute the information processing capacity of the simple repression motif. These data are separated by the operator and repressor copy number we examined. Please see the main text or the paper website at https://mrazomej.github.io/chann_cap/analysis for...
Microscopy image files for \"First-principles prediction of the information processing capacity of a simple genetic circuit.\"Manuel Razo-Mejia, Rob Phillips, Sarah Marzen, Rachel Taubman, Muir Morrison & Griffin Chure
These data correspond to the raw microscopy images used to quantify fluorescence and compute gene expression distributions due to the activity of the Lac repressor molecule in E. coli cells. These images were passed through an image analysis pipeline which segmented individual cells and computed the mean pixel value for each cell. These data are separated by the operator we examined. A single strain was measured in twelve different inducer concentrations for each dataset with...
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.
Data from: High-molecular-weight polymers from dietary fiber drive aggregation of particulates in the murine small intestineAsher Preska Steinberg, Sujit S. Datta, Thomas Naragon, Justin C. Rolando, Said R. Bogatyrev & Rustem F. Ismagilov
The lumen of the small intestine (SI) is filled with particulates: microbes, therapeutic particles, and food granules. The structure of this particulate suspension could impact uptake of drugs and nutrients and the function of microorganisms; however, little is understood about how this suspension is re-structured as it transits the gut. Here, we demonstrate that particles spontaneously aggregate in SI luminal fluid ex vivo. We find that mucins and immunoglobulins are not required for aggregation. Instead,...
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.
Persistence of neuronal representations through time and damage in the hippocampus.Walter Gonzalez
Raw and processed data used in the manuscript. Also included are the custom MATLAB scripts used.
Detrital zircon ages of Sespe Formation orthoquartzitesLeah Sabbeth
Detrital zircon ages from orthoquartzite clasts in the Sespe Formation
Summary tables for 2019 release of JCAP Materials Experiment and Analysis DatabaseJohn Gregoire & Edwin Soedarmadji
Plate.csv containing 1 row for each plate and composition.csv containing 1 row for each composition sample described in the seminal public release of the JCAP Materials Experiment and Analysis Database, described in publication "Tracking materials science data lineage to manage millions of materials experiments and analyses", doi: 10.1038/s41524-019-0216-x with web interface hosted at https://htejcap.org or https://doi.org/10.25989/es8t-kswe
Synaptic organization of cortico-cortical communication in primatesMaria Ashaber, Laszlo Zalanyi, Emese Palfi, Istvan Stuber, Tamas Kovacs, Rob M. Friedman, Anna W. Roe & László Négyessy
In cortical circuitry synaptic communication across areas is based on two types of axon terminals, small and large, with modulatory and driving roles, respectively. In contrast, it is not known whether similar synaptic specializations exist for intra-areal projections. Using anterograde tracing and three-dimensional reconstruction by electron microscopy (3D-EM) we asked if large boutons form synapses in the circuit of somatosensory cortical areas 3b and 1. In contrast to observations in macaque visual cortex, light microscopy...
Replication data for \"Reevaluation of Perchlorate in Gale Crater Rocks Suggests Geologically Recent Perchlorate Addition\"Peter Martin
Laboratory data generated in support of the manuscript titled "Reevaluation of Perchlorate in Gale Crater Rocks Suggests Geologically Recent Perchlorate Addition" in the Journal of Geophysical Research: Planets. Additional data may be found in the NASA PDS. See manuscript for details of data collection.
Raman and X-Ray Diffraction Data for Acetylene ClathrateTuan H. Vu
Data behind figures for J. Phys. Chem. A 2019, 123, 7051-7056
Segmentation of the Main Himalayan Thrust illuminated by Bayesian inference of interseismic coupling
This dataset contains GPS data, Leveling data, and the fault geometry used for the inversions.
Individual Bedding Fit Measurements on Vera Rubin Ridge
This table contains derived attitude measurements corresponding to traces of individual beds in the Vera Rubin Ridge. Measurements were performed on stereo Mastcam images assuming a 3 sigma stereo error standard deviation.
Signatures of the r-process in Ancient Stellar Populations Using Barium AbundancesGina Duggan
Machine readable tables from Chapter 2 of the thesis titled "Signatures of the r-process in Ancient Stellar Populations Using Barium Abundances".
JPL Mars Yard DatabaseYumi Iwashita, Kazuto Nakashima, Adrian Stoica, Ryo Kurazume & Sir Rafol
JPL Mars Yard Database is built to understand terrain types from various sensors, such as RGB and IR. It has 2 datasets; 1. Semantic Dataset 1: Understanding Terrain Types from RGB and IR, 2. Virtual Sensor Dataset 1: Deriving RGB-to-IR mapping models. Both datasets were collected at JPL Mars Yard on Nov. 17th 2017, with a RGB camera (FLIR Grasshopper 5M) and a thermal camera (FLIR AX65). We collected images every 1 hour, from 10...
Persistence of neuronal representations through time and damage in the hippocampusWalter Gonzalez
MATLAB scripts and design files for the project described in ...
MD&A statements from public firms: 2002-2018Michael Ewens
Text and headers from MD&A sections found in public firm 10-K statements. Follow these directions to get the data in a form that can be analyzed: https://github.com/michaelewens/MD-A-10K
Western Pacific Model Subduction ZonesMichael Gurnis, Pengfei Ma, Shaofeng Liu & Bo Zhang
netCDF files for cross sections in the western Pacific through spherical models of plate tectonics and mantle convection