AndreaBozzo/ceres-open-data-index huggingface dataset:
Rodent Research-1 (RR1) NASA Validation Flight: Mouse adrenal gland 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: animal-and-tissue-sampling, animal-husbandry, data-transformation, dna-sequencing-library-construction, genelab-rnaseq-data-processing-protocol, labeling, library-construction, mass-spectrometry, mouse-habitation, nucleic-acid-extraction, nucleic-acid-sequencing, protein-extraction, rna-sequencing-library-construction, sample-collection, spaceflight, tmt-isobaric-labeling
Organization: National Aeronautics and Space Administration
Characterization of Epigenetic Regulation in an Extraterrestrial Environment: The Arabidopsis Spaceflight Methylome [Bisulfite-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 x92s future space exploration goals.

Tags: bisulfite-seq-library-construction, bisulfite-seq-nucleic-acid-extraction, bisulfite-seq-nucleic-acid-sequencing, bisulfite-seq-sequence-analysis-data-transformation, growth-protocol, organism-part, spaceflight, treatment-protocol
Organization: National Aeronautics and Space Administration
The influence of simulated microgravity on the proteome of Daphnia magna

Background/Objectives: The waterflea Daphnia is an interesting candidate for bioregenerative life support systems (BLSS). These animals are particularly promising because of their central role in the limnic food web and its mode of reproduction. However the response of Daphnia to altered gravity conditions has to be investigated especially on the molecular level to evaluate the suitability of Daphnia for BLSS in space. Methods: In this study we applied a proteomic approach to identify key proteins and pathways involved in the response of Daphnia to simulated microgravity generated by a 2D-clinostat. We analysed 5 biological replicates using 2D-DIGE proteomic analysis. Results: We identified 109 protein spots differing in intensity (p < 0.05). Substantial fractions of these proteins are involved in actin microfilament organisation indicating the disruption of cytoskeletal structures during clinorotation. Furthermore proteins involved in protein folding were identified suggesting altered gravity induced breakdown of protein structures in general. In addition simulated microgravity increased the abundance of energy metabolism related proteins indicating an enhanced energy demand of Daphnia. Conclusion: The affected biological processes were also described in other studies using different organisms and systems either aiming to simulate microgravity conditions or providing real microgravity conditions. Moreover most of the Daphnia protein sequences are well conserved throughout taxa indicating that the response to altered gravity conditions in Daphnia follows a general concept.

Tags: data-collection, data-transformation, electrophoresis, extraction, labeling, mass-spectrometry, normalization, protein-extraction, sample-collection, weightlessness-simulation
Organization: National Aeronautics and Space Administration
The Effects of Spaceflight Factors on the Human Plasma Proteome, Including Both Real Space Missions and Ground-Based Experiments

The aim of the study was to continue of the proteomic data accumulation on the effects of space flight factors on the human body, including ground-based model experiments. Blood plasma samples were collected from 5 healthy men included in the 21 days head-down bed rest experiment (HDBR) and 5 volunteers participating in a 21 day long dry immersion experiment.

Tags: sample-collection-extraction-mass-spectrometry-data-transformation, spaceflight-bed-rest-time-dry-immersion
Organization: National Aeronautics and Space Administration
RNA-Seq transcriptome analysis of reactive oxygen species gene network in Mizuna plants grown in long-term space flight

Space environment is suspected to generate reactive oxygen species (ROS) and induce oxidative stress in plants however little is known about the gene expression of ROS gene network in plants grown in long-term space flight. RNA-Seq was used to define the large-scale gene expression profiles of Mizuna harvested after 27 days cultivation in the international space station to understand the molecular response and adaptation to space environment.Results: Total reads of transcripts from the Mizuna grown in the international space station as well as on the ground by RNA-Seq using next generation sequencing technology showed 8,258 and 14,170 transcripts up- and down-regulated in the space-grown Mizuna respectively when compared with those from the ground-grown Mizuna. A total of 20 in 32 ROS oxidative marker genes were up-regulated including high expression of 4 hallmarks and preferentially expressed gene associated with ROS-scavenging genes was thioredoxin glutaredoxin and alternative oxidase genes. In the transcription factors of ROS gene network MEKK1-MKK4-MPK3 OXI1-MKK4-MPK3 and OXI1-MPK3 of MAP cascades induction of WRKY22 by MEKK1-MKK4-MPK3 cascade induction of WRKY25 and repression of ZAT7 by Zat12 were suggested. RbohD and RbohF genes were up-regulated preferentially in NADPH oxidase genes which produce ROS.Conclusions: Our large-scale transcriptome analysis demonstrated that the space environment induced oxidative stress and ROS gene network was activated in the space-grown Mizuna some of which were common genes up-regulated by abiotic and biotic stress and were preferentially up-regulated genes by the space environment even though Mizuna grew in the space as well as on the ground showing that plants could acclimate to the space environment by reprograming the expression of ROS gene network.

Tags: data-transformation, genelab-rnaseq-data-processing-protocol, library-construction, nucleic-acid-extraction, nucleic-acid-sequencing, sample-collection, spaceflight
Organization: National Aeronautics and Space Administration
The Arabidopsis spaceflight transcriptome: a comparison of whole plants to discrete root hypocotyl and shoot responses to the orbital environment

Arabidopsis thaliana was evaluated for its response to the spaceflight environment in three replicated experiments on the International Space Station. Two approaches were used; GFP reporter genes were used to collect gene expression data in real time within unique GFP imaging hardware and plants were harvested on orbit to RNAlater for subsequent analyses of gene expression with using Affymetrix and SAGE transcriptome analyses. Three tissue types were examined (leaves hypocotyls and roots) and compared to analyses conducted with whole plants. Transcriptome analyses with whole plants suggested that the spaceflight environment had little impact on the transcriptome of arabidopsis however closer examination of selected tissues revealed that there are a number of tissue-specific responses that arabidopsis employs to respond to this novel environment

Tags: bioassay_data_transformation, data-transformation, genelab-microarray-data-processing-protocol, grow, hybridization, labeling, nucleic_acid_extraction, organism-part, p-mtab-28101, p-mtab-28102, p-mtab-28103, p-mtab-28104, p-mtab-28105, p-mtab-28106, p-mtab-28107, reverse_transcription, spaceflight
Organization: National Aeronautics and Space Administration
Inflammatory gene expression signatures in idiopathic intracranial hypertension: possible implications in microgravity-induced ICP elevation - Plasma

The visual impairment and intracranial pressure (VIIP) syndrome is a neuro-ophthalmologic condition described in astronauts returning from long duration space missions. Idiopathic intracranial hypertension (IIH), also known as pseudotumor cerebri, is characterized by a chronic elevation of intracranial pressure (ICP) in the absence of an intracranial mass lesion. Because VIIP and IIH share some neurologic and ophthalmologic manifestations, the latter might be used as a model to study some of the processes underlying VIIP. This work constitutes a preliminary investigation of the molecular pathways associated with the elevation of ICP in IIH. Gene expression signatures were obtained from exosomes collected from CSF and plasma in patients with possible signs of IIH. The gene expression targets focused on inflammatory genes and miRNAs. The results suggest that inflammatory cytokine-driven processes and immune cell migration are activated when ICP is elevated in IIH patients, either as a cause or effect of the ICP increase. Several miRNAs appear to be involved in this response, among which miR-9 and miR-16 are upregulated in CSF and plasma of higher ICP subjects. This study provides evidence in support of neurophysiological alterations and neuro-immunomodulation in this condition. If similar changes are seen in astronauts manifesting with the VIIP syndrome, an underlying pathophysiological basis may be discovered.

Tags: intracranial-pressure, sample-collection-nucleic-acid-extraction-reverse-transcribed-pcr-mrna-qpcr-mrna-array-reverse
Organization: National Aeronautics and Space Administration
Gene expression data from 4T1 irradiated tumors treated with TGFbeta blockade

Accumulating data support the concept that ionizing radiation therapy (RT) has the potential to convert the tumor into an in situ individualized vaccine; however this potential is rarely realized by RT alone. Transforming growth factor  xce xb2 (TGF xce xb2) is an immunosuppressive cytokine that is activated by RT and inhibits the antigen-presenting function of dendritic cells and the differentiation of effector CD8+ T cells. Here we tested the hypothesis that TGF xce xb2 hinders the ability of RT to promote anti-tumor immunity. Development of tumor-specific immunity was examined in a pre-clinical model of metastatic breast cancer. Mice bearing established 4T1 mouse mammary carcinoma treated with pan-isoform specific TGF xce xb2 neutralizing antibody 1D11 showed significantly improved control of the irradiated tumor and non-irradiated metastases but no effect in the absence of RT. Notably whole tumor transcriptional analysis demonstrated the selective upregulation of genes associated with immune-mediated rejection only in tumors of mice treated with RT+TGF xce xb2 blockade. Mice treated with RT+TGF xce xb2 blockade exhibited cross-priming of CD8+ T cells producing IFN xce xb3 in response to three tumor-specific antigens in tumor-draining lymph nodes which was not evident for single modality treatment. Analysis of the immune infiltrate in mouse tumors showed a significant increase in CD4+ and CD8+ T cells only in mice treated with the combination of RT+TGF xce xb2 blockade. Depletion of CD4+ or CD8+ T cells abrogated the therapeutic benefit of RT+TGF xce xb2 blockade. These data identify TGF xce xb2 as a master inhibitor of the ability of RT to generate an in situ tumor vaccine which supports testing inhibition of TGF xce xb2 during radiotherapy to promote therapeutically effective anti-tumor immunity. We used genome-wide microarray to depict main biological processes responsibles for the therapeutic benefit of the combination ofTGF-beta blockade and local radiotherapy. To gain a more comprehensice protrait of the effects of RT and TGFbeta blockade on gene expressionin tumors we collected 4T1 tumors 4 days after completion of RT. Three tumors from each group were then subjected to RNA extraction and hybridization on affymetrix array.

Tags: array-scanning-protocol, data-transformation, genelab-microarray-data-processing-protocol, growth-protocol, hybridization-protocol, ionizing-radiation, labelling-protocol, normalization-data-transformation-protocol, nucleic-acid-extraction-protocol, p-gse61208-1, p-gse61208-2, p-gse61208-3, p-gse61208-4, p-gse61208-5, p-gse61208-6, p-gse61208-7, sample-treatment-protocol, treatment
Organization: National Aeronautics and Space Administration
Microarray Analysis of Space-flown Murine Thymus Tissue

Microarray Analysis of Space-flown Murine Thymus Tissue Reveals Changes in Gene Expression Regulating Stress and Glucocorticoid Receptors. We used microarrays to detail the gene expression of space-flown thymic tissue and identified distinct classes of up-regulated genes during this process. We report here microarray gene expression analysis in young adult C57BL/6NTac mice at 8 weeks of age after exposure to spaceflight aboard the space shuttle (STS-118) for a period of 13 days. Upon conclusion of the mission thymus lobes were extracted from space flown mice (FLT) as well as age- and sex-matched ground control mice similarly housed in animal enclosure modules (AEM). mRNA was extracted and an automated array analysis for gene expression was performed. Examination of the microarray data revealed 970 individual probes that had a 1.5 fold or greater change. When these data were averaged (n=4) we identified 12 genes that were significantly up- or down-regulated by at least 1.5 fold after spaceflight (p < 0.05). Together these data demonstrate that spaceflight induces significant changes in the thymic mRNA expression of genes that regulate stress glucocorticoid receptor metabolism and T cell signaling activity. These data explain in part the reported systemic compromise of the immune system after exposure to the microgravity of space.

Tags: cosmic-radiation, data-transformation, genelab-microarray-data-processing-protocol, growth-protocol, labeling, normalization-data-transformation, nucleic-acid-hybridization, radiation-dosimetry, rna-extraction, scan-protocol, spaceflight, treatment-protocol
Organization: National Aeronautics and Space Administration
Impact of spaceflight on gene expression in the thymus

The thymus undergoes atrophy during spaceflight. In this study we analyzed gene expression of the thymus of mice on board International space station to elucidate molecular aspects of the thymic atrophy by spaceflight.

Tags: altered-gravity, animal-husbandry, data-transformation, experiment, genelab-rnaseq-data-processing-protocol, library-construction, mouse-habitation, nucleic-acid-extraction, nucleic-acid-sequencing, sample-collection, spaceflight
Organization: National Aeronautics and Space Administration
miRNA signature detection and countermeasures against HZE radiation exposure for tissue degeneration-Soleus muscle

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
Effects of 21 days of bedrest on human skeletal muscle gene expression

The present study concerns the effects of 21 days of sustained recumbence (bedrest) on skeletal muscle gene expression. 14 male subjects participated in normoxic bedrest (NBR) with muscle unloading for 21 days this is a substudy of tha PlanHab-study which apart from normoxic bedrest also involved hypoxic bedrest and hypoxic ambulation. Throughout both bedrest interventions each subject remained in a horizontal position at all times. He was allowed one pillow for the head and to occasionally lean on an elbow while eating or being transferred to a gurney. Muscular exercise was prohibited. During the HAMB confinement each subject was allowed to move freely within the hypoxic area. To mimic a normal level of physical activity subjects performed 30 minutes of low-to-moderate-intensity exercise twice daily. Muscle samples from Vastus lateralis.

Tags: bed-rest, labeling, normalization-data-transformation, nucleic-acid-hybridization, rna-extraction, sample-collection, sampling-time, scan-protocol, treatment-protocol
Organization: National Aeronautics and Space Administration
Goddard Institute for Space Studies

Research at the NASA Goddard Institute for Space Studies (GISS) emphasizes a broad study of global change, which is an interdisciplinary initiative addressing natural and man-made changes in our environment that occur on various time scales from one-time forcings such as volcanic explosions, to seasonal and annual effects such as El Nino, and on up to the millennia of ice ages and that affect the habitability of our planet.

Tags: aerosols, astrophysics, climate, climate-index, clouds, earth-science, electromagnetic, energy, oceans, precipitation, radiative-flux, simulations, storms, temperature
Organization: National Aeronautics and Space Administration
Microarray Analysis of Space-flown Murine Thymus Tissue

Microarray Analysis of Space-flown Murine Thymus Tissue Reveals Changes in Gene Expression Regulating Stress and Glucocorticoid Receptors. We used microarrays to detail the gene expression of space-flown thymic tissue and identified distinct classes of up-regulated genes during this process. We report here microarray gene expression analysis in young adult C57BL/6NTac mice at 8 weeks of age after exposure to spaceflight aboard the space shuttle (STS-118) for a period of 13 days. Upon conclusion of the mission thymus lobes were extracted from space flown mice (FLT) as well as age- and sex-matched ground control mice similarly housed in animal enclosure modules (AEM). mRNA was extracted and an automated array analysis for gene expression was performed. Examination of the microarray data revealed 970 individual probes that had a 1.5 fold or greater change. When these data were averaged (n=4) we identified 12 genes that were significantly up- or down-regulated by at least 1.5 fold after spaceflight (p?0.05). Together these data demonstrate that spaceflight induces significant changes in the thymic mRNA expression of genes that regulate stress glucocorticoid receptor metabolism and T cell signaling activity. These data explain in part the reported systemic compromise of the immune system after exposure to the microgravity of space.

Tags: absorbed-radiation-dose, growth-protocol, labeling, mesh-gravitation, normalization-data-transformation, nucleic-acid-hybridization, radiation-detection, radiation-dosimetry, rna-extraction, scan-protocol
Organization: National Aeronautics and Space Administration
Comparative proteomic analysis and bioluminescent reporter gene assays to investigate effects of simulated microgravity on Caco-2 cells

Microgravity is one of the most important features in spaceflight. Previous evidence has shown that significant changes to the musculoskeletal and immune systems occurred under microgravity. The present study was undertaken to explore the change in protein abundance in human colon colorectal cells that were incubated for 48 or 72 h either in normal conditions and µG simulated conditions. The comparative proteomic method based on the 18O labeling technique was applied to investigate the up-regulated proteins and down-regulated proteins in SH-SY5Y under simulated microgravity.

Tags: microgravity-simulation-tiime, treatment-protocol-extraction-mass-spectrometry
Organization: National Aeronautics and Space Administration