AndreaBozzo/ceres-open-data-index huggingface dataset:
Inflammatory gene expression signatures in idiopathic intracranial hypertension: possible implications in microgravity-induced ICP elevation - CSF

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, sample-collection-nucleic-acid-extraction-reverse-transcribed-pcr-qpcr-mrna-array-reverse-trans
Organization: National Aeronautics and Space Administration
Goddard Robotic Telescope (GRT)

Since it is not possible to predict when a Gamma-Ray Burst (GRB) occurs, the follow-up ground telescopes must be distributed as uniform as possible all over the world in order to collect simultaneous data with the Swift detections. Based on the three-year operations of Swift, however, we noticed the distinct gap in follow-up coverage in the eastern U.S. region (Figure 1). This fact motivated us to construct a fully automated optical telescope here at GSFC.

Tags: active-galactic-nuclei, gamma-ray-bursts, grt, jet-physics, robotics, telescope
Organization: National Aeronautics and Space Administration
Rodent Research-1 (RR1) NASA Validation Flight: Mouse tibialis anterior 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: animal-and-tissue-sampling, animal-husbandry, data-transformation, dna-library-construction, epitranscriptomics, genelab-rnaseq-data-processing-protocol, labeling, library-construction, mass-spectrometry, mouse-habitation, nucleic-acid-extraction, nucleic-acid-sequencing, protein-extraction, rna-methylation-analysis, rna-sequencing-library-construction, sample-collection, spaceflight, tmt-isobaric-labeling
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 AEM-X 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: data-transformation, labeling, library-construction, mass-spectrometry, microgravity, nucleic-acid-extraction, nucleic-acid-sequencing, protein-extraction, sample-collection, spike-in-control, spike-in-control-protocol, treatment
Organization: National Aeronautics and Space Administration
Rodent Research-1 (RR1) NASA Validation Flight: Mouse tibialis anterior 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
Dissecting transcriptional responses of nucleolin mutants to red light stimulation and darkness in ground reference conditions

Understanding plant adaptive responses to the space environment is a requisite for enabling space farming. Spaceflight produce deleterious effects on plant cells particularly affecting ribosome biogenesis a complex stress-sensitive process coordinated with cell division and differentiation known to be activated by red light. Here we have used mutants from the two nucleolin genes in Arabidopsis (NUC1 and NUC2) encoding the main regulator of the ribosome biogenesis in the nucleolus in order to better understand their role in adaptive response mechanisms to stress. Thus we show that nucleolin stress-related gene NUC2 can compensate the environmental stress provided by darkness in nuc1 plants while nuc2 plants are not able to provide a complete response to red light. These ground control findings as part of the ESA/NASA Seedling Growth spaceflight experiments will determine the basis for the identification of a genetic background enabling an adaptive advantage for plants in future space experiments.

Tags: genotype, library-construction, light, nucleic-acid-extraction, nucleic-acid-sequencing, treatment-protocol
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: library-construction, nucleic-acid-extraction, nucleic-acid-sequencing, sample-collection, space-flight
Organization: National Aeronautics and Space Administration
An environment with strong gravitational and magnetic field alterations synergizes to promote variations in Arabidopsis thaliana callus global transcriptional state

Using diamagnetic levitation we have exposed A. thaliana in vitro callus cultures to five environments with different levels of effective gravity (from levitation i.e. simulated mg* to 2g*) and magnetic fields (10.1 to 16.5 Tesla) and we have compared the results with those of similar experiments done in a Random Position Machine (simulated micro g) and a Large Diameter Centrifuge (2g) free of high magnetic fields. Microarray analysis indicates that there are changes in overall gene expression of the cultured cells exposed to these unusual environments but also that gravitational and magnetic field produce synergic variations in the steady state of the transcriptional profile of A. thaliana. Significant changes in the expression of structural abiotic stress and secondary metabolism genes were observed into the magnet field. These results confirm that the strong magnetic field both at micro g* or 2g* has a significant effect on the expression of these genes but subtle gravitational effects are still observable. These subtle responses to microgravity environments are opposite to the ones observed in a hypergravity one. seven-condition experiment MM2D Arabidopsis culture callus control vs. Treatment (altered gravity simulation GBF). Three GBF were used (LDC (2g) + control RPM (mg) + control and Magnet (mg* 0.1g* 1g* 1.9g* 2g*) + control). Biological replicates: 3 replicates in all conditions and controls except 1.9g* (2 replicates)

Tags: bioassay_data_transformation, feature_extraction, grow, hybridization, image_aquisition, labeling, nucleic_acid_extraction, p-gse29787-1, p-gse29787-2, p-gse29787-3, p-gse29787-4, p-gse29787-5, p-gse29787-6, p-gse29787-7, p-gse29787-8, sample-type, specified_biomaterial_action, treatment
Organization: National Aeronautics and Space Administration
Galactic cosmic radiation induces stable epigenome alterations relevant to human lung cancer

Human deep space and planetary travel is limited by uncertainties regarding the health risks associated with exposure to galactic cosmic radiation (GCR) and in particular the high linear energy transfer (LET) heavy ion component. Here we assessed the impact of two high-LET ions 56Fe and 28Si and low-LET X rays on genome-wide methylation patterns in human bronchial epithelial cells. We found that all three radiation types induced rapid and stable changes in DNA methylation but at distinct subsets of CpG sites affecting different chromatin compartments. The 56Fe ions induced mostly hypermethylation and primarily affected sites in open chromatin regions including enhancers promoters and edges (  shores  ) of CpG islands. The 28Si ion-exposure had mixed effects inducing both hyper and hypomethylation and affecting sites in more repressed heterochromatic environments whereas X rays induced mostly hypomethylation primarily at sites in gene bodies and intergenic regions. Significantly the methylation status of 56Fe ion irradiation sensitive sites but not those affected by X ray or 28Si ions could discriminate tumor from normal tissue for human lung adenocarcinomas and squamous cell carcinomas. Thus high LET radiation exposure leaves a lasting imprint on the epigenome and affects sites relevant to human lung cancer. The 56Fe ion signature may prove useful in monitoring the cumulative biological impact and associated cancer risks encountered by astronauts in deep space. Genome wide DNA methylation profiling of normal human bronchial epithelial cells irradiated with varying doses of 28Si-ion radiation ( 300 MeV/u at 0 0.3 1.0 Gy)  56Fe-ion radiation (600 MeV/u at 0 0.1 0.3 1.0 Gy) or X rays (320 kV at 0 1.0 Gy). Triplicate control and irradiated samples were incubated and sampled at 4 timepoints between 2 and 62 days. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across >485,000 CpGs from collected samples. Samples include: 56Fe ions 4 doses x 4 time points x 3 replicates (4 removed in QC) = 44 samples; 28Si ions = 3 doses x 4 time points x 3 replicates = 36 samples; X ray 2 doses x 4 time points x 3 replicates (2 removed in QC)= 22 samples. Overall design: Bisulphite converted DNA from the 102 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip.

Tags: cell-growth, data-collection, dna-extraction, dose, growth, ionizing-radiation, labeling, methylation, normalization-data-transformation, nucleic-acid-hybridization, sample-collection, time, treatment
Organization: National Aeronautics and Space Administration
Genetic Dissection of the Spaceflight Transcriptome Responses in Plants: are some responses unnecessary?

Experimentation on the International Space Station has reached the stage where repeated and nuanced transcriptome studies are beginning to illuminate the structural and metabolic differences between plants grown in space compared to plants on the Earth. Genes that are important in setting up the spaceflight responses are being identified; their role in spaceflight physiological adaptation are increasingly understood and the fact that different genotypes adapt differently is recognized. However the basic question of whether these spaceflight responses are required for survival has yet to be posed and the fundamental notion that spaceflight responses may be non-adaptive has yet to be explored. Therefore the experiments presented here were designed to ask if portions of the plant spaceflight response can be genetically removed without causing loss of spaceflight survival and without causing increased stress responses. The CARA experiment compared the spaceflight transcriptome responses of two Arabidopsis ecotypes Col-0 and WS as well as that of a PhyD mutant of Col-0. When grown with the ambient light of the ISS phyD displayed a significantly reduced spaceflight transcriptome response compared to Col-0 suggesting that altering the activity of a single gene can actually improve spaceflight adaptation by reducing the transcriptome cost of physiological adaptation. The WS genotype showed an even simpler spaceflight transcriptome response in the ambient light of the ISS more broadly indicating that the plant genotype can be manipulated to reduce the transcriptome cost of plant physiological adaptation to spaceflight and suggesting that genetic manipulation might further reduce or perhaps eliminate the metabolic cost of spaceflight adaptation. When plants were germinated and then left in the dark on the ISS the WS genotype actually mounted a larger transcriptome response than Col-0 suggesting that the in-space light environment affects physiological adaptation which further implies that manipulating the local habitat can also substantially impact the metabolic cost of spaceflight adaptation.

Tags: data-transformation, ecotype, genelab-rnaseq-data-processing-protocol, growth-protocol, library-construction, light-treatment, nucleic-acid-extraction, nucleic-acid-sequencing, sequence-analysis-data-transformation, spaceflight
Organization: National Aeronautics and Space Administration
Transcription profiling of activated human T cells induced by microgravity to identify apoptotic genes and other immune response genes

The purpose of this study was to search for microgravity-sensitive genes specifically for apoptotic genes influenced by the microgravity environment and other genes related to immune response. Experiment Overall Design: Two-group design with paired samples i.e. one 1G and one MMG culture came from the same donor. Therefore 6 samples came from 3 different donors. Experiment Overall Design: Donor 1 :GSM96146,GSM96147 Experiment Overall Design: Donor 2: GSM96148 GSM96149 Experiment Overall Design: Donor 3: GSM96150,GSM96151 Experiment Overall Design: Total RNA was submitted to and then labeled hybridized and data generated by the Baylor College Medicine Microarray Core Facility (333E One Baylor Plaza Houston TX 77030).

Tags: data-processing-protocol, hybridization-protocol, labeling-protocol, nucleic-acid-extraction-protocol, sample-collection-protocol, scan-protocol, simulated-microgravity
Organization: National Aeronautics and Space Administration
Exposure of zebrafish larvae to 3g and 5g hyper gravity between 5-6 days post-fertilization.

The general objective of the study was to determine modulation of gene expression by environmental factors with a special emphasis on bone formation. For this reason the specific period of treatment was chosen between 5-6 days post-fertilization (dpf) when bone formation and calcification are taking place. Zebrafish larvae were placed at 5 dpf into a Large Diameter Centrifuge and brought to a gravitational force of 3g or 5g for 24 hours. We show that this treatment causes a clear increase of bone formation as illustrated by cranial skeleton staining of the bone matrix by Alizarin Red by morphometric analysis of the resulting images and by gene expression studies of selected genes. Thus a whole genome micro-array experiment was conducted to identify genes that may be involved in the observed effect on bone formation.

Tags: array-scanning-and-feature-extraction-protocol, growth-protocol, hypergravity, normalization-data-transformation-protocol, nucleic-acid-extraction-protocol, nucleic-acid-hybridization-to-array-protocol, nucleic-acid-labeling-protocol, p-mtab-43156, p-mtab-43157, p-mtab-43158, p-mtab-43159, p-mtab-43160, p-mtab-43161, p-mtab-43162, stimulus, treatment-protocol
Organization: National Aeronautics and Space Administration
Dynamic gene expression response to altered gravity in human T cells (parabolic flight)

We investigated differentially regulated genes in human Jurkat T lymphocytic cells in 20s and 5min microgravity and in hypergravity and compared expression profiles to identify potential gravity-regulated genes and adaptation processes.

Tags: growth-protocol, hypergravity, labeling, microgravity, normalization-data-transformation, nucleic-acid-hybridization, nucleic-acid-hybridization-to-array-protocol, rna-extraction, scan-protocol, treatment-protocol
Organization: National Aeronautics and Space Administration
RNAseq analysis of the response of Arabidopsis thaliana phytochrome mutants (PhyA PhyB) to fractional gravity under blue-light stimulation during spaceflight

Traveling to nearby extraterrestrial objects having a reduced gravity level (partial gravity) compared to Earth s gravity is becoming a realistic objective for space agencies. The use of plants as part of life support systems will require a better understanding of the interactions among plant growth responses including tropisms under partial gravity conditions. Here we present results from the Seedling Growth space experiments on the ISS to complement the previously released GLDS-251 dataset including seeds of Arabidopsis thaliana wildtype plants. Seeds were germinated and seedlings grew for six days under different gravity levels namely micro-g several intermediate partial-g levels and 1g and were subjected to irradiation with blue light for the last 48 hours. RNA was extracted was obtained for 20 wildtype samples for subsequent RNAseq analysis in GLDS-251 here we add 36 samples from similarly exposed PhyA and PhyB mutants.

Tags: genotype-spaceflight-altered-gravity-light, treatmemt-protocol-nucleic-acid-extraction-spike-in-protocol-library-construction-nucleic-acid
Organization: National Aeronautics and Space Administration
Draft Genome Sequences of Acinetobacter and Bacillus Strains Isolated from Spacecraft-Associated Surfaces

We report here the draft genome sequences of four strains isolated from spacecraft-associated surfaces exhibiting increased resistance to stressors such as UV radiation and exposure to H2O2. The draft genomes of strains 1P01SC, FO-92, 50v1, and 2P01AA had sizes of 5,500,894 bp, 4,699,376 bp, 3,174,402 bp, and 4,328,804 bp, respectively.

Tags: sample-collection-nucleic-acid-sequencing-sequence-assembly, sample-location
Organization: National Aeronautics and Space Administration