AndreaBozzo/ceres-open-data-index huggingface dataset:
A study of gene expression influenced by simulated microgravity in human lymphoblastoid cells

Here in this study we systematically examined the patterns of DNA methylation and hydroxy-methylation with its functional implications in gene regulation for the cultured TK6 lymphoblastoid cells upon exposure to micro-gravity conditions. The results reported here indicate that simulated microgravity alters methylation patterns in a limited way and subsequently the expression of genes involved in stress response like ATF3 FBXO17 MAP3K13 and VCL in TK6 cells. Overall design: Examination of RNA-seq with 2 replicates each for 1 cell type

Tags: nucleic-acid-extraction-library-construction-nucleic-acid-sequencing-sequence-analysis-data-tra, weightlessness-simulation
Organization: National Aeronautics and Space Administration
National Space Science Data Center Master Catalog

The National Space Science Data Center serves as the permanent archive for NASA space science mission data. 'Space science' means astronomy and astrophysics, solar and space plasma physics, and planetary and lunar science. As permanent archive, NSSDC teams with NASA's discipline-specific space science 'active archives' which provide access to data to researchers and, in some cases, to the general public. Search by event, spacecraft, experiment, map, or publication query. NSSDC is part of the Solar System Exploration Data Services Office (SSEDSO) in the Solar System Exploration Division at NASA's Goddard Space Flight Center in Greenbelt, MD.

Tags: astronomy, astrophysics, heliophysics, lunar-science, nssdc, planetary-science, space-plasma-physics, space-science
Organization: National Aeronautics and Space Administration
During development the Sku6 mutant roots engage different genes than wild type Col-0 roots either on the ground or in spaceflight.

The wild type Col-0 plants and the Sku-6 mutant plants of the Col-0 background were germinated on ISS or on the ground and the gene expression profiles in roots at 4 days or 8 days were established. The Sku6 gene (At2g03680) codes for a protein that localizes to microtubule within the cortical array and putatively acting as an intramolecular linker. The development of Col-0 and Sku-6 plants on orbit differs from that on the ground as demonstrated by the comparison of the gene expression profiles between 4 days old to 8 days old plant in the two environments. However the development of Sku-6 mutant plants also differs from Col-0 at either age and in either environment suggesting the role of the genetic background in these developmental decisions. The 4 days old Sku-6 roots in orbit engaged more genes than the 4 days old Col-0 roots in orbit but also more than the 4 days old Sku-6 roots on the ground. Overall the 4 days old roots differentially expressed more genes in spaceflight relative to ground than the 8 days old roots of either genotype.

Tags: genotype, growth, library-construction, nucleic-acid-extraction, nucleic-acid-sequencing, sample-collection, sequence-analysis-data-transformation, spaceflight, time
Organization: National Aeronautics and Space Administration
Mars surface image (Curiosity rover) labeled data set version 1

This data set consists of 6691 images spanning 24 classes that were collected by the Mars Science Laboratory (MSL, Curosity) rover by three instruments (Mastcam Right eye, Mastcam Left eye, and MAHLI). These images are the "browse" version of each original data product, not full resolution. They are roughly 256x256 pixels each. We divided the MSL images into train, validation, and test data sets according to their sol (Martian day) of acquisition. This strategy was chosen to model how the system will be used operationally with an image archive that grows over time. The images were collected from sols 3 to 1060 (August 2012 to July 2015). The exact train/validation/test splits are given in individual files. Full-size images can be obtained from the PDS at https://pds-imaging.jpl.nasa.gov/search/ .

Tags: machine-learning, mahli, mars, mars-science-laboratory, mastcam, planetary-science, usg-artificial-intelligence
Organization: National Aeronautics and Space Administration
Mouse fecal microbiome after exposure to high LET radiation

Space travel is associated with continuous low-dose-rate exposure to high Linear Energy Transfer (LET) radiation. Pathophysiological manifestations after low-dose radiation exposure are strongly influenced by non-cytocidal radiation effects including microbiome and cellular gene expression. Using a mouse model for exposure to high LET radiation we observed substantial changes in the composition and functional potential of the microbiome. These were paralleled by changes in the abundance of multiple metabolites which were related to the enzymatic activity of the altered metagenome by means of metabolic network modeling. There was a complex dynamic in microbial and metabolic composition at different radiation doses suggestive of transient dose-dependent interactions between microbial ecology and signals from the host  s cellular damage repair processes. Functional shifts included features associated with dysbiosis at the onset of chronic inflammatory responses which could prMouse fecal microbiome after exposure to high LET radiatione-dispose space travelers to systemic long-term health risks.

Tags: dose, irradiation, library-construction, nucleic-acid-extraction, nucleic-acid-sequencing, sample-collection, timepoint
Organization: National Aeronautics and Space Administration
Swabs from the International Space Station Raw sequence reads

16S sequencing of 15 swabs from the International Space Station

Tags: sample-collection-nucleic-acid-extraction-library-construction-nucleic-acid-sequencing-data-tra, sample-collection-nucleic-acid-extraction-library-construction-nucleic-acid-sequencing-genelab, spaceflight-sample-location
Organization: National Aeronautics and Space Administration
LAT 2-year Point Source Catalog Aperture Photometry Lightcurves

Due to a glitch in the analysis pipeline there are apparent increases in flux around MJD 56810 for many sources. These increases are *not* real and should be disregarded. The problem is now believed to be fixed, and the most recent flux measurements are expected to be correct. At a later date the light curves will be reprocessed to remove these incorrect data points.

Tags: acd, balloon, bursts, cgro, compton, egret, energy, fermi, gamma, gamma-ray, glast, glast-ssc, gro, gssc, high-energy
Organization: National Aeronautics and Space Administration
NASA Engineering Network Lessons Learned

The NASA Lessons Learned system provides access to official, reviewed lessons learned from NASA programs and projects. These lessons have been made available to the public by the NASA Office of the Chief Engineer and the NASA Engineering Network. Each lesson describes the original driving event and provides recommendations that feed into NASA’s continual improvement via training, best practices, policies, and procedures.

Tags: ares-1-x, foia, geophysical, hq, technical-reports, transparency, xml
Organization: National Aeronautics and Space Administration
Fermi LAT GRBs

All analysis results presented here are preliminary and are not intended as an official catalog of Fermi-LAT detected GRBs. Please consult the table's caveat page for analysis details and other important information.

Tags: acd, balloon, bursts, cgro, compton, egret, energy, fermi, gamma, gamma-ray, glast, glast-ssc, gro, gssc, high-energy
Organization: National Aeronautics and Space Administration
Equipotential Shape Models for the Gas Giants

This dataset contains geopotential shape models of Jupiter and Saturn derived from the high-precision gravitational field models produced by the Juno mission to Jupiter and Cassini's Grand Finale at Saturn. This dataset is intended to be paired with the following article submitted to the Journal of Geophysical Research-Planets:

Buccino, Dustin R., Ravit Helled, Marzia Parisi, William Hubbard, and
William Folkner, "Updated Geopotential Shapes of Jupiter and Saturn using
Juno and Cassini Grand Finale Gravity Science Measurements", Journal of
Geophysical Research, 2020 (submitted Jan 2020).
 
This dataset of shape models was produced in part at the Jet Propulsion Laboratory by the Juno Gravity Instrument Team and Interiors Working Group.

Tags: cassini, juno, jupiter, saturn
Organization: National Aeronautics and Space Administration
Bacillus subtilis spores PROTECT experiment Space-exposed and Mars-exposed vs. Earth-control

Because of their ubiquity and resistance to spacecraft decontamination bacterial spores are considered likely potential forward contaminants on robotic missions to Mars. Thus it is important to understand their global responses to long-term exposure to space or Mars environments. As part of the PROTECT experiment spores of B. subtilis 168 were exposed to real space conditions and to simulated martian conditions for 559 days in low Earth orbit mounted on the EXPOSE-E exposure platform outside the European Columbus module on the International Space Station. Upon return spores were germinated total RNA extracted and fluorescently labeled and used to probe a custom Bacillus subtilis microarray to identify genes preferentially activated or repressed relative to ground control spores. Increased transcript levels were detected for a number of stress-related regulons responding to DNA damage (SOS response SP-beta prophage induction) protein damage (CtsR/Clp system) oxidative stress (PerR regulon) and cell envelope stress (SigV regulon). Spores exposed to space demonstrated a much broader and more severe stress response than spores exposed to simulated Mars conditions. The results are discussed in the context of planetary protection for a hypothetical journey of potential forward contaminant spores from Earth to Mars and their subsequent residence on Mars. Two-color microarrays were performed comparing germination of Space-exposed or Mars-exposed vs. ground-control (Earth) spores.

Tags: bioassay_data_transformation, environment-exposure, feature_extraction, gravitation, grow, hybridization, image_aquisition, labeling, nucleic_acid_extraction, p-gse37124-1, p-gse37124-2, p-gse37124-3, p-gse37124-4, p-gse37124-5, p-gse37124-6, p-gse37124-7, p-gse37124-8, specified_biomaterial_action
Organization: National Aeronautics and Space Administration
Comparative gene expression analysis in the Arabidopsis thaliana root apex using RNA-seq and microarray transcriptome profiles

The root apex is an important section of the plant root involved in environmental sensing and cellular development. Analyzing the gene profile of root apex in diverse environments is important and challenging especially when the samples are limiting and precious such as in spaceflight. The feasibility of using tiny root sections for transcriptome analysis was examined in this study. To understand the gene expression profiles of the root apex Arabidopsis thaliana Col-0 roots were sectioned into Zone-I (0.5 mm root cap and meristematic zone) and Zone-II (1.5 mm transition elongation and growth terminating zone). Gene expression was analyzed using microarray and RNA seq. Both the techniques arrays and RNA-Seq identified 4180 common genes as differentially expressed (with > two-fold changes) between the zones. In addition 771 unique genes and 19 novel TARs were identified by RNA-Seq as differentially expressed which were not detected in the arrays. Single root tip zones can be used for full transcriptome analysis; further the root apex zones are functionally very distinct from each other. RNA-Seq provided novel information about the transcripts compared to the arrays. These data will help optimize transcriptome techniques for dealing with small rare samples.

Tags: data-collection, data-transformation, genelab-microarray-data-processing-protocol, genelab-rnaseq-data-processing-protocol, growth-protocol, labeling, library-construction, normalization-data-transformation, nucleic-acid-hybridization, nucleic-acid-sequencing, rna-extraction, root-zone, sample-collection, sequence-analysis-data-transformation
Organization: National Aeronautics and Space Administration
Sentinel-3A OLCI Regional Mapped Inland Waters (ILW) Data, version 4

The Inland Waters dataset (ILW) provides data for lakes and other water bodies across the contiguous United States (CONUS) and Alaska. ILW significantly reduces the processing effort required by end users and is a standardized community resource for lake and reservoir algorithm development and performance assessment. The data is provided for 15,450 CONUS waterbodies with a size of at least one 300 m pixel and over 2,300 resolvable lakes with sizes greater than three 300 m pixels. Alaska has 5,874 lakes resolvable lakes. ILW was developed in collaboration with the Cyanobacteria Assessment Network (CyAN). Additional inland water details and resources, including maps of resolvable lakes and additional inland water products, such as true color imagery, are available at the CyAN site.

Tags: aquatic-sciences, bacteria-archaea, biological-classification, biosphere, coastal-processes, earth-science, earth-science-services, ecosystems, environmental-advisories, environmental-governance-management, human-dimensions, hydrological-advisories, marine-environment-monitoring, ocean-optics, oceans, surface-water, terrestrial-hydrosphere, water-quality-water-chemistry
Organization: National Aeronautics and Space Administration
Solar Dynamics Observatory

A searchable database of all Solar Dynamics Observatory data including EUV, magnetograms, visible light and X-ray.  SDO: The Solar Dynamics Observatory is the first mission to be launched for NASA's Living With a Star (LWS) Program, a program designed to understand the causes of solar variability and its impacts on Earth. SDO is designed to help us understand the Sun's influence on Earth and Near-Earth space by studying the solar atmosphere on small scales of space and time and in many wavelengths simultaneously.  SDO's goal is to understand, driving towards a predictive capability, the solar variations that influence life on Earth and humanity's technological systems by determining how the Sun's magnetic field is generated and structured and how this stored magnetic energy is converted and released into the heliosphere and geospace in the form of solar wind, energetic particles, and variations in the solar irradiance.

Tags: curiosity, heliophysics, sdo, solar, space-science, sun, wise
Organization: National Aeronautics and Space Administration
Dynamic gene expression response to altered gravity in human myelomonocytic U937 cells [sounding rocket]

We investigated differentially regulated genes in human myelomonocytic U937 cells in 20s and 5min microgravity and in hypergravity and compared expression profiles to identify potential gravity-regulated genes and adaptation processes. Overall design: Human myelomonocytic U937 cells were exposed to altered gravity during a sounding rocket mission.

Tags: altered-gravity, data-collection, growth, labeling, normalization-data-transformation, nucleic-acid-hybridization, rna-extraction, sample-collection, treatment
Organization: National Aeronautics and Space Administration
Genechip analysis of bone marrow osteoprogenitors exposed to microgravity

In March 2006 murine Bone Marrow Stromal Cells (BMSC) were flown in the Soyuz 12S to the International Space Station to investigate the effects of microgravity on their osteogenic potential in a three-dimensional environment. BMSC were grown in porous bioceramic Skelite disks (dia 9 mm x T 1.2 mm). The constructs were exposed to microgravity for ca. 8 days then fixed for RNA extraction. While the flight experiment was performed in fully automated hardware inside the KUBIK incubator one group of control samples were incubated inside manually operated hardwares (flight control) and the other control group was incubated under routine laboratory conditions (lab control). The altered gene expression profile was analyzed by Mouse Gene 1.0 ST array (Affymetrix) representing whole-transcript coverage. Each one of the 28853 genes is represented on the array by approximately 26 probes spread across the full length of the gene providing a more complete and more accurate picture of gene expression than the 3   based expression array design. A few days of microgravity were sufficient to determinate at least at the molecular level an effect in the BMSC; this response expressed a stress condition able to determinate consequences on several compartments and cellular functions. In particular it seems to promote a gene expression known to be associated with neurogenic activity (e.g. axon guidance) perhaps promoting the BMSC capability to be committed in that direction. The osteo-induction by dexamethasone-based medium due to the short duration of stimulation did not have the possibility to manifest itself at the phenotypic level but only partially at the molecular level.

Tags: altered-gravity, data-transformation, feature_extraction, genelab-microarray-data-processing-protocol, grow, hybridization, image_aquisition, labeling, nucleic_acid_extraction, p-gse17696-2, p-gse17696-3, p-gse17696-5, p-gse17696-6, p-gse17696-7, p-gse17696-8, p-gse17696-9, p-gse17698-4, spaceflight, specified_biomaterial_action, treatment
Organization: National Aeronautics and Space Administration
Gene expression response to simulated gravity and hypergravity in human T cells

We investigated differentially regulated and stably expressed genes in human Jurkat T lymphocytic cells in 5min simulated microgravity and hypergravity and compared expression profiles to identify gravity-regulated and unaffected genes as well as adaptation processes. This dataset is part of a series of three and the other two datasets are deposited in GLDS-172 and GLDS-188.

Tags: growth-protocol, hypergravity, labeling, microgravity, normalization-data-transformation, nucleic-acid-hybridization, rna-extraction, scan-protocol, treatment-protocol
Organization: National Aeronautics and Space Administration
miRNA signature detection and countermeasures against HZE radiation exposure for tissue degeneration-Liver tissue

Biological risks associated with space radiation and microgravity are major concerns for long-term space travel. Through a Systems Biology approach our previous NASA work has shown both TGF xce xb2 signaling pathways and miRNAs have a critical impact on defining health risks with and without space irradiation. We hypothesize that circulating microRNA (miRNA) signatures are driving microvascular disease and muscle degeneration associated with accelerating aging and will be enhanced by exposure to the space environment (radiation and microgravity). We investigated this hypothesis both in vivo and in vitro and test novel antagonist therapies to these miRNA signatures as countermeasures to reduce space radiation-induced health risks. A comprehensive Systems Biology approach was used to examine the influence by high atomic number by high (H) atomic number (Z) and energy (E) (HZE) irradiation. To simulate low-dose exposure due to galactic cosmic rays (GCR) we used the ions energy and doses determined by a NASA consensus formula of 7 different ions to represent GCR (referred to as GCR sim model). To simulate high-dose radiation exposure due to solar particle events (SPE) we used an acute dose of SPE simulated beam at 1Gy which has energies ranging from 50MeV to 150MeV. C57BL/6 wild-type mice were utilized for irradiation with our established simulated microgravity model (hindlimb suspension model) and an in vitro 3D microvasculature tissue model under simulated microgravity (clinostat) conditions will also be irradiated. To expand on the circulating miRNA signature determined from our preliminary data we determined a group of conserved miRNAs which are commonly being regulated in the majority of the organs and tissues throughout the host using our established techniques. MiRNA-sequencing on serum (before IR and at time of sacrifice) liver heart and muscle tissue for all radiation groups revealed the key circulating miRNA signature (consisting of multiple miRNAs) impacting disease risk. Collectively understanding of how whole body space radiation impacts microvascular and tissue degeneration through circulating miRNAs will greatly enhance health risk prognostication and provide possible new mechanisms for protection against space radiation.

Tags: hindlimb-unloading, ionizing-radiation, library-construction, nucleic-acid-extraction, nucleic-acid-sequencing, treatment-protocol
Organization: National Aeronautics and Space Administration
Mars orbital image (HiRISE) labeled data set version 3

This data set contains a total of 73,031 landmarks. 10,433 landmarks were detected and extracted from 180 HiRISE browse images, and 62,598 landmarks were augmented from 10,433 original landmarks. For each original landmark, we cropped a square bounding box that includes the full extent of the landmark plus a 30-pixel margin to left, right, top and bottom. Each cropped landmark was resized to 227x227 pixels, and then was augmented to generate 6 additional landmarks using the following methods:

1. 90 degrees clockwise rotation
2. 180 degrees clockwise rotation
3. 270 degrees clockwise rotation
4. Horizontal flip
5. Vertical flip
6. Random brightness adjustment

Tags: hirise, machine-learning, mars-reconnaissance-orbiter, planetary-science, usg-ai-training-data, usg-artificial-intelligence
Organization: National Aeronautics and Space Administration
Biological Research in Canisters-16 (BRIC-16): Investigations of the plant cytoskeleton in microgravity with gene profiling and cytochemistry

These investigations studied the fundamentals of how plants perceive gravity and develop in microgravity. It informs how gene regulation is altered by spaceflight conditions.

Tags: data-collection, data-processing, labeling, microgravity, nucleic-acid-hybridization, rna-extraction, sample-collection
Organization: National Aeronautics and Space Administration
Global gene expression profiling of radiation-induced rat mammary carcinomas

To investigate gene expression patterns in rat mammary carcinomas induced by ionizing radiation. Gene expression patterns were analyzed in radiation-induced rat mammary carcinomas and normal mammary gland tissues.

Tags: animal-husbandry, data-collection, data-transformation, housing, ionizing-radiation, labeling, normalization-data-transformation, nucleic-acid-hybridization, rna-extraction, tissue, treatment-protocol
Organization: National Aeronautics and Space Administration
Expression data from SPHINX (SPaceflight of Huvec: an INtegrated eXperiment)

Changes in the physical environment modulate cell responses and may lead to the impairment or even failure of tissue function as a result of mechanotransduction processes. It has been suggested that this situation occurs in some age-related diseases and some pathological conditions observed in space such as cardiovascular deconditioning bone loss muscle atrophy and impaired immune responses. All of these are associated with endothelial dysfunction but the precise mechanism is still unclear. We used the microarray approach to obtain insights into the mechanism responsible for endothelial dysfunction by taking advantage of the challenging environment of gravitational unloading onboard the International Space Station. The effects of gravitational unloading on HUVEC gene expression were investigated by means of cDNA microarray analyses of six randomly chosen samples (three for each of the two conditions of spaceflight and 1g) using Affymetrix Gene Human 1.0 ST Arrays

Tags: bioassay_data_transformation, data-transformation, feature_extraction, genelab-microarray-data-processing-protocol, grow, hybridization, image_aquisition, labeling, nucleic_acid_extraction, p-gse43582-1, p-gse43582-2, p-gse43582-3, p-gse43582-4, p-gse43582-5, p-gse43582-6, p-gse43582-7, p-gse43582-8, spaceflight, specified_biomaterial_action
Organization: National Aeronautics and Space Administration