AndreaBozzo/ceres-open-data-index huggingface dataset:
Rodent Research-1 (RR1) NASA Validation Flight: Mouse gastrocnemius muscle transcriptomic proteomic and epigenomic data

NASA  s Rodent Research (RR) project is playing a critical role in advancing biomedical research on the physiological effects of space environments. Due to the limited resources for conducting biological experiments aboard the International Space Station (ISS) it is imperative to use crew time efficiently while maximizing high-quality science return. NASA  s GeneLab project has as its primary objectives to 1) further increase the value of these experiments using a multi-omics systems biology-based approach and 2) disseminate these data without restrictions to the scientific community. The current investigation assessed viability of RNA DNA and protein extracted from archived RR-1 tissue samples for epigenomic transcriptomic and proteomic assays. During the first RR spaceflight experiment a variety of tissue types were harvested from subjects snap-frozen or RNAlater-preserved and then stored at least a year at -80C after return to Earth. They were then prioritized for this investigation based on likelihood of significant scientific value for spaceflight research. All tissues were made available to GeneLab through the bio-specimen sharing program managed by the Ames Life Science Data Archive and included mouse adrenal glands quadriceps gastrocnemius tibialis anterior extensor digitorum longus soleus eye and kidney. We report here protocols for and results of these tissue extractions and thus the feasibility and value of these kinds of omics analyses. In addition to providing additional opportunities for investigation of spaceflight effects on the mouse transcriptome and proteome in new kinds of tissues our results may also be of value to program managers for the prioritization of ISS crew time for rodent research activities.

Tags: 5mc-total-rna-methylation-analysis, animal-and-tissue-sampling, dna-library-construction, epitranscriptomics, labeling, library-construction, mass-spectrometry, microgravity, nucleic-acid-extraction, nucleic-acid-sequencing, protein-extraction, proteomic-labeling, rna-library-construction, sample-collection
Organization: National Aeronautics and Space Administration
T Cell Activation in Microgravity Compared to 1g (Earth  s) Gravity

This study tested the hypothesis that transcription of immediate early genes is inhibited in T cells activated in microgravity (uG). Immunosuppression during spaceflight is a major barrier to safe long-term human space habitation and travel. The goals of these experiments were to prove that uG was the cause of impaired T cell activation during spaceflight as well as understand the mechanisms controlling early T cell activation. T cells from 4 human donors were stimulated with concanavalin A (ConA) and anti-CD28 onboard the International Space Station (ISS). An onboard centrifuge was used to generate a 1g simultaneous control to isolate the effects of uG from other variables of spaceflight. Microarray expression analysis after 1.5 hours of activation demonstrated that mg- and 1g-activated T cells had distinct patterns of global gene expression and identified 47 genes that were significantly differentially down-regulated in uG. Importantly several key immediate early genes were inhibited in uG. T cells were isolated from human volunteers. T cells from each donor were kept separate and loaded into individual chambers in separate cassettes for the following treatments: uG non-activated uG activated and 1g activated. Therefore samples represent biological triplicates. Experimental units were launched into space and placed into the KUBIK facility onboard the International Space Station. The 1g units were placed in the central centrifuge positions and centrifuged with an applied 1g force. The uG units were place in the static positions for continued uG exposure. After 30 minutes of pre-incubation uG non-activated units were fixed by addition of RNALater (QIAGEN Valencia CA) removed from the incubator and stored in 4 xc2 xb0C. The uG and 1g activated units were injected with final concentration 10mg/ml Con A and 4mg/ml anti-CD28. These cassettes were replaced into KUBIK on either the centrifuge or static positions and activated for 1.5 hours. Activation was stopped with the addition of RNALater and the units were then moved to 4 xc2 xb0C storage. All units were returned to Earth for analysis.

Tags: data-transformation, genelab-microarray-data-processing-protocol, grow, hybridization, image_aquisition, labeling, microgravity-simulation, nucleic_acid_extraction, p-gse38836-2, p-gse38836-3, p-gse38836-4, p-gse38836-5, p-gse38836-6, p-gse38836-7, spaceflight, specified_biomaterial_action, treatment
Organization: National Aeronautics and Space Administration
OrbView-2 SeaWiFS 4M Global Mapped Garver-Siegel-Maritorena Model (GSM) Data, version R2022.0

The SeaWiFS instrument was launched by Orbital Sciences Corporation on the OrbView-2 (a.k.a. SeaStar) satellite in August 1997, and collected data from September 1997 until the end of mission in December 2010. SeaWiFS had 8 spectral bands from 412 to 865 nm. It collected global data at 4 km resolution, and local data (limited onboard storage and direct broadcast) at 1 km. The mission and sensor were optimized for ocean color measurements, with a local noon (descending) equator crossing time orbit, fore-and-aft tilt capability, full dynamic range, and low polarization sensitivity.

Tags: earth-science, ocean-optics, oceans
Organization: National Aeronautics and Space Administration
Impact of Antiorthostatic Suspension on Mouse response to Tetanus Toxoid and CpG

These data were generated from mice that were skeletally unloaded using antiorthostatic suspension (AOS). Mice were either subjected to AOS or tail restraint without unloading for two weeks before injection with saline xc2 xb1tetanus toxoid xc2 xb1Cpg. Mice were unloaded for an additional two weeks before being sacrificed.

Tags: animal-treatment, animal-treatmet, hindlimb-unloading, nucleic-acid-extraction, nucleic-acid-sequencing, rna-sequencing-library-construction, sample-collection, tetanus-toxoid, vaccine-adjuvant
Organization: National Aeronautics and Space Administration
Rodent Research-3-CASIS: Mouse kidney transcriptomic proteomic and epigenomic data

The Rodent Research-3 (RR-3) mission was sponsored by the pharmaceutical company Eli Lilly and Co. and the Center for the Advancement of Science in Space to study the effectiveness of a potential countermeasure for the loss of muscle and bone mass that occurs during spaceflight. Twenty BALB/c 18-weeks old female mice (ten controls and ten treated) were flown to the ISS and housed in the Rodent Habitat for 39-42 days. Twenty mice of similar age sex and strain were used for ground controls housed in identical hardware and matching ISS environmental conditions. Basal controls were housed in standard vivarium cages. Spaceflight ground controls and basal groups had blood collected then were euthanized had one hind limb removed and finally whole carcasses were stored at -80 C until dissection. All mice in this data set received only the control/sham injection.

Tags: animal-husbandry, data-transformation, genelab-rnaseq-data-processing-protocol, labeling, library-construction, mass-spectrometry, mouse-habitation, nucleic-acid-extraction, nucleic-acid-sequencing, protein-extraction, sample-collection, sequencing-library-construction, spaceflight, spike-in-control, spike-in-control-protocol, tmt-isobaric-labeling
Organization: National Aeronautics and Space Administration
Characterization of Epigenetic Regulation in an Extraterrestrial Environment: The Arabidopsis Spaceflight Methylome [RNA-seq]

When germinated and grown on-board the ISS (International Space Station) plant do not exhibit abnormal structures but they do have altered growth habits and this project aims to investigate the molecular mechanisms that provide the foundation for the altered growth habits observed in orbit. APEX03-2 (Advanced Plant Experiment 03-2) also known as TAGES-ISA (Transgenic Arabidopsis Gene Expression System-Intracellular Signaling Architecture) specifically addresses the growth and molecular changes that occur in Arabidopsis thaliana plants during spaceflight by using molecular and genetic tools and by asking fundamental questions regarding root structure growth and cell wall remodeling may be answered. This investigation advances the fundamental understanding of the molecular biological responses to extraterrestrial environments. This understanding helps to further define the impacts of spaceflight on biological systems to better enable NASA xc3 xaf xc2 xbf xc2 xbds future space exploration goals.

Tags: data-transformation, genelab-rnaseq-data-processing-protocol, organism-part, rna-seq-library-construction, rna-seq-nucleic-acid-extraction, rna-seq-nucleic-acid-sequencing, rna-seq-sequence-analysis-data-transformation, spaceflight, treatment-protocol
Organization: National Aeronautics and Space Administration
Synergistic effects of space radiation and microgravity (miRNA WT and dys-mutant)

Space radiations and microgravity both could cause DNA damage in cells but the effects of microgravity on DNA damage response to space radiations are still controversial. A mRNA microarray and microRNA microarray in dauer larvae of Caenorhabditis elegans (C. elegans) that endured spaceflight environment and space radiations environment during 16.5-day Shenzhou-8 space mission were performed. In our study wild type and dys-1 mutant strains of C.elegans endured four conditions during shenzhou-8 spaceflight mission including spaceflight static condition(ss) spaceflight 1-g centrifugal condition(sc) ground control condition(gc) and no-transport control. Limited to the quantity of worm samples we performed technical-repeat test but not sample-repeat test. Accordingly eight miRNA microarrays were performed.

Tags: absorbed-radiation-dose, data-collection, labeling, normalization-data-transformation, nucleic-acid-hybridization, rna-extraction, sample-collection, weightlessness
Organization: National Aeronautics and Space Administration
Mouse femur LC-MSMS upon weightlessness

Bone loss and immune dysregulation are among the main adverse outcomes of spaceflight challenging astronaut xe2 x80 x99s health and safety. However consequences on B cell development and responses are still under-investigated. Up to now most studies addressing these questions were performed using an amphibian species. Consequently we used advanced proteomics analysis of femur bone and marrow of mice flown for one month on board the BION-M1 biosatellite to determine whether extreme conditions encountered during a real spaceflight affect B cell development in mice and to examine reversibility of the effects upon return to Earth. Our data revealed that adverse effects on B lymphopoiesis were more marked one week after landing and that this phenomenon was associated with a 41% reduction of B cells in the spleen. Thus the effects of spaceflight persisted during at least one week after landing. These reductions may contribute to explain increased susceptibility to infection even if we confirmed that animals were able to mount a humoral immune response.

Tags: animal-and-tissue-sampling, animal-husbandry, extraction, mass-spectrometry, mouse-habitation, sample-collection, spaceflight, time
Organization: National Aeronautics and Space Administration
Worms spun in centrifuge at elevated g values

Worms spun at higher than normal g values for 4 days on 20G centrifuge vs. worms kept at 1 X G. Both are mixed stage cultures. A stimulus or stress experiment design type is where that tests response of an organism(s) to stress/stimulus. e.g. osmotic stress behavioral treatment Physical Characteristics: worms kept at increased g values for 4 days (x g value) stimulus_or_stress_design

Tags: array-scanning-protocol, gravity-altered, hybridization-protocol, labelling-protocol, normalization-data-transformation-protocol, nucleic-acid-extraction-protocol, p-gse38877-1, p-gse38877-2, p-gse38877-3, p-gse38877-4, p-gse38877-5, p-gse38877-6, sample-treatment-protocol
Organization: National Aeronautics and Space Administration
Transcriptomic analysis of quadriceps from mice subjected to simulated spaceflight euthanasia freezing and tissue preservation protocols

To understand the molecular mechanisms affected by spaceflight it is essential to achieve high quality sample preservation on-orbit for downstream gene expression analysis. However sample preservation protocols must also be compatible with available equipment and crew time. NASA  s Rodent Research (RR) missions have used various methods for euthanasia carcass preservation and tissue preservation. This study extends the sample preservation study performed by GeneLab in GLDS-49 which examined conditions used for the RR-1 mission to include conditions used for multiple RR missions and is designed to help determine factors which may confound data analysis. To determine whether these various factors affect changes in gene expression this ground-based study generated gene expression profiles measured by RNAseq from the quadriceps of 20-21 week-old female C57BL/6J mice. Multiple interacting factors were investigated: 1) To understand how euthanasia protocols affect gene expression when mouse carcasses are slow frozen mice were euthanized by either euthasol injection ketamine/xylazine injection or CO2 inhalation and carcasses slow frozen on dry-ice mimicking carcass preservation in the MELFI on the ISS. Carcasses were thawed and RNA extracted from quadriceps; 2) To understand how carcass preservation protocols affect gene expression mice were euthanized with euthasol and carcasses preserved by flash freezing in liquid nitrogen slow freezing on dry ice or immersion in RNAlater following three-way segmentation. Carcasses were thawed and RNA extracted from quadriceps; 3) To understand how tissue preservation protocols affect gene expression mice were euthanized with euthasol and quadriceps immediately dissected and preserved by flash freezing in liquid nitrogen slow freezing on dry ice or immersion in RNAlater.

Tags: carcass-preservation-method, data-transformation, dissection-condition, euthanasia, euthanasia-animal, euthanasia-method, genelab-rnaseq-data-processing-protocol, library-construction, nucleic-acid-extraction, nucleic-acid-sequencing, sample-collection, spike-in-control, spike-in-control-protocol, tissue-preservation-method
Organization: National Aeronautics and Space Administration
Transcription profiling of Arabidopsis seedings exposed to UV-B irradiation

Interaction of COP1 and UVR8 which regulate UV-B-induced photomorphogenesis and stress acclimation in Arabidopsis thaliana.

Tags: data-collection, data-transformation, genotype, growth-protocol, labeling, light, nucleic-acid-hybridization, p-mtab-2659, p-mtab-2661, p-mtab-2662, p-mtab-2664, p-mtab-2665, p-mtab-2666, p-mtab-2669, p-mtab-2671, p-mtab-2672, p-mtab-2674, p-mtab-2676, p-mtab-2677, rna-extraction, time, treatment
Organization: National Aeronautics and Space Administration
Low dose ionizing radiation treated lymphoblastoid cells

Irradiated cell lines exposed to 1-10 Gy 2 Lymphoblastoid cell lines (GM15510 and GM15036) irradiated 1 2.5 5 7.5 10 Gy RNA is isolated and labeled using a T7 amplification Arcturus kit for hybridization on triplicate arrays.

Tags: bioassay_data_transformation, cell-line, dose, feature_extraction, grow, hybridization, image_aquisition, ionizing-radiation, labeling, nucleic_acid_extraction, p-gse22639-1, p-gse22639-2, p-gse22639-3, p-gse22639-4, p-gse22639-5, p-gse22639-6, p-gse22639-7, p-gse22639-8, specified_biomaterial_action
Organization: National Aeronautics and Space Administration
Thermosphere-Ionosphere Modeling with Forecastable Inputs: Case Study of the June 2012 High Speed Stream Geomagnetic Storm

This is the companion dataset for the Journal paper ”Thermosphere-Ionosphere Modeling With Forecastable Inputs: Case Study of the June 2012 High Speed Stream Geomagnetic Storm” (under review). The dataset contains raw outputs from a global ionosphere-thermosphere model for a geomagnetic storm events. The outputs are in IDL binary format, containing the model solution of the total electron content, the magnetic field, density, velocity, and temperature for neutral and ion species. The outputs are analyzed in the paper to evaluate the forecast capability of the model.

Tags: geomagnetism, ionosphere-magnetosphere-dynamics
Organization: National Aeronautics and Space Administration
Rodent Research-1 (RR1) NASA Validation Flight: Mouse liver transcriptomic proteomic and epigenomic data

RR-1 is a validation flight to evaluate the hardware operational and science capabilities of the Rodent Research Project on the ISS. RNA DNA and protein were purified from liver tissues from RR-1 mice (female C57BL/6J 16wk old at time of launch). From each group two liver samples were collected and frozen immediately after euthanasia. The rest of the liver samples from each group were collected from frozen carcasses dissected post-flight. RNA-Seq whole genome and RNA BS-Seq (bisulfite sequencing) and proteomic expression profiling were performed.  xc2 xa0RNA extracted from these tissues was re-sequenced; these data are available as part of GLDS-168 (https://genelab-data.ndc.nasa.gov/genelab/accession/GLDS-168). xc2 xa0

Tags: 5mc-total-rna-methylation-analysis, dissection-condition, dna-library-construction, epitranscriptomics, extraction, labeling, library-construction, mass-spectrometry, mass-spectrometry-protocol, mouse-habitation, mouse-habitation-protocol, nucleic-acid-extraction, nucleic-acid-sequencing, protein-extraction, proteomics-data-transformation, rna-sequencing-library-construction, sample-collection, spaceflight, tmt-isobaric-labeling
Organization: National Aeronautics and Space Administration
Improved Simulations of Biomass Burning Aerosol Optical Properties and Lifetimes during the ORACLES-I Campaign: Results from the NASA GEOS Model

This dataset contains model results and satellite-based research retrievals associated with the manuscript submitted in Atmospheric Chemistry and Physics Journal, titled, " Improved Simulations of Biomass Burning Aerosol Optical Properties and Lifetimes in the NASA GEOS Model during the ORACLES-I Campaign".

There were multiple NASA GEOS global model simulations performed for this study. Following are the name of the simulation and their description corresponding to the file names within this dataset:

1. Baseline: Default version of the GEOS model
2. Smoke Age: Default version of the GEOS model run with biomass burning OA tagged by day of the week it was emitted.
3. Smoke Composition: Default version of the GEOS model run with biomass burning OA tagged by type of vegetation burned.
4. OA-loss: Hydrophilic OA from biomass burning is assigned a 6-day e-folding loss time; OA from biomass burning sources is enhanced 60%, BC from biomass burning sources is enhanced 15%.
5. OA-loss+updated optics: As in OA-loss but with updated aerosol optical properties.

Tags: aerosols, global-model
Organization: National Aeronautics and Space Administration
Synergistic effects of space radiation and microgravity (miRNA WT and ced-1 mutant)

Space radiations and microgravity both could cause DNA damage in cells but the effects of microgravity on DNA damage response to space radiations are still controversial. A mRNA microarray and microRNA microarray in dauer larvae of Caenorhabditis elegans (C. elegans) that endured space xef xac x82ight environment and space radiations environment during 16.5-day Shenzhou-8 space mission were performed. In our study wild type and ced-1 mutant strains of C.elegans endured three conditions during shenzhou-8 spaceflight mission including spaceflight static condition(ss) spaceflight 1-g centrifugal condition(sc) and ground control condition(gc). Limited to the quantity of worm samples we performed technical-repeat test but not sample-repeat test.Accordingly xef xbc x8csix miRNA microarrays were performed.

Tags: absorbed-radiation-dose, data-collection, labeling, normalization-data-transformation, nucleic-acid-hybridization, rna-extraction, sample-collection, weightlessness
Organization: National Aeronautics and Space Administration
Synergistic effects of microgravity and space radiation (Nimblegen)

Space radiations and microgravity both could cause DNA damage in cells but the effects of microgravity on DNA damage response to space radiations are still controversial. A mRNA microarray and microRNA microarray in dauer larvae of Caenorhabditis elegans (C. elegans) that endured spaceflight environment and space radiations environment during 16.5-day Shenzhou-8 space mission were performed. In our study wild type dys-1 mutant and ced-1 mutant strains of C.elegans endured four conditions during shenzhou-8 spaceflight mission including spaceflight static condition(ss) spaceflight 1-g centrifugal condition(sc) ground control condition(gc) and no-transport control. Limited to the quantity of worm samples we performed technical-repeat test but not sample-repeat test.Accordingly 12 mRNA microarrays were performed.

Tags: absorbed-radiation-dose, data-collection, labeling, normalization-data-transformation, nucleic-acid-hybridization, rna-extraction, sample-collection, weightlessness
Organization: National Aeronautics and Space Administration
miRNA signature detection and countermeasures against HZE radiation exposure for tissue degeneration-Plasma

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