AndreaBozzo/ceres-open-data-index huggingface dataset:
Global gene expression analysis highlights microgravity sensitive key genes in soleus and EDL of 30 days space flown mice

Microgravity exposure as well as chronic muscle disuse are two of the main causes of physiological adaptive skeletal muscle atrophy in humans and murine animals in physiological condition. The aim of this study was to investigate at both morphological and global gene expression level skeletal muscle adaptation to microgravity in mouse soleus and extensor digitorum longus (EDL). Adult male mice C57BL/N6 were flown aboard the BION-M1 biosatellite for 30 days on orbit (BF) or housed in a replicate flight habitat on Earth (BG) as reference flight control. In this study we investigated for the first time gene expression adaptation to 30 days of microgravity exposure in mouse soleus and EDL highlighting potential new targets for improvement of countermeasures able to ameliorate or even prevent microgravity-induced atrophy in future spaceflights. Overall Design: C57BL/N6 mice were randomly divided in 3 groups: Bion Flown (BF) mice flown aboard the Bion M1 biosatellite in microgravity environment for 30 days; Bion Ground (BG) mice housed in the same habitat of flown animals but exposed to earth gravity; and Flight Control (FC) mice housed in a standard animal facility.

Tags: cosmic-radiation, data-collection, data-transformation, genelab-microarray-data-processing-protocol, labeling, mouse-habitation, normalization-data-transformation, nucleic-acid-hybridization, radiation-dosimetry, rna-extraction, sample-collection, spaceflight, tissue
Organization: National Aeronautics and Space Administration
Global gene expression analysis highlights microgravity sensitive key genes in soleus and EDL of 30 days space flown mice

Microgravity exposure as well as chronic muscle disuse are two of the main causes of physiological adaptive skeletal muscle atrophy in humans and murine animals in physiological condition. The aim of this study was to investigate at both morphological and global gene expression level skeletal muscle adaptation to microgravity in mouse soleus and extensor digitorum longus (EDL). Adult male mice C57BL/N6 were flown aboard the BION-M1 biosatellite for 30 days on orbit (BF) or housed in a replicate flight habitat on Earth (BG) as reference flight control. In this study we investigated for the first time gene expression adaptation to 30 days of microgravity exposure in mouse soleus and EDL highlighting potential new targets for improvement of countermeasures able to ameliorate or even prevent microgravity-induced atrophy in future spaceflights. Overall Design: C57BL/N6 mice were randomly divided in 3 groups: Bion Flown (BF) mice flown aboard the Bion M1 biosatellite in microgravity environment for 30 days; Bion Ground (BG) mice housed in the same habitat of flown animals but exposed to earth gravity; and Flight Control (FC) mice housed in a standard animal facility.

Tags: data-collection, labeling, microgravity, normalization-data-transformation, nucleic-acid-hybridization, rna-extraction, sample-collection
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: ionizing-radiation-dose-time-of-sample-collection-after-treatment, sample-collection-nucleic-acid-extraction-library-construction-nucleic-acid-sequencing-data-tra, sample-collection-nucleic-acid-extraction-library-construction-nucleic-acid-sequencing-genelab
Organization: National Aeronautics and Space Administration
Transcription profiling of rat to study the effect of hindlimb unloading on healing of medial collateral ligaments 3 weeks after injury

A recent physiological study established that hindlimb unloading of rats at 3 and 7 weeks inhibits healing of injured ligaments resulting in a badly aligned discontinuous collagen matrix. Using tissue from these rats we focused on the 3-week time point employing microarray analysis to identify what cellular processes or lack of processes could account for these observed deficiencies. We used the Affymetrix RG_U34A GeneChip and performed image analysis with Microarray Suite 5.0. For normalization we used the MAS global normalization protocol with a default target mean signal of 500. Gene expression in medial collateral ligament tissue under 4 different treatment conditions was measured: loaded control loaded wound healing unloaded control and unloaded wound healing. From our results it appears that unloaded tissue lags behind loaded tissue in its progression through the healing process and at 3 weeks is still engaged in the proliferative phase whereas loaded tissue is actively remodeling its collagen matrix.

Tags: affymetrix-protocol-hybridization-unknown, clinical-treatment, feature_extraction, hybridization, p-affy-6, protocoltype
Organization: National Aeronautics and Space Administration
Monthly Near-Surface Air Temperature Averages

Global surface temperatures in 2010 tied 2005 as the warmest on record. The International Satellite Cloud Climatology Project (ISCCP) was established in 1982 as part of the World Climate Research Programme (WCRP) to collect and analyze the global distribution of clouds, their properties, and their diurnal, seasonal, and interannual variations. The LAS provides data for Monthly Near-Surface Air Temperature Averages from 1994 to 2008.

Tags: apps, arctic-sea-ice, carbon-dioxide, climate, electricity, ephemerides, geodetics, land-ice, news, radar, waves
Organization: National Aeronautics and Space Administration
FERMIGBRST - Fermi GBM Burst Catalog

This table lists all of the triggers observed by a subset of the 14 GBM detectors (12 NaI and 2 BGO) which have been classified as gamma-ray bursts (GRBs). Note that there are two Browse catalogs resulting from GBM triggers. All GBM triggers are entered in the Fermi GBM Trigger Catalog, while only those triggers classified as bursts are entered in the Burst Catalog. Thus, a burst will be found in both the Trigger and Burst Catalogs. The Burst Catalog analysis requires human intervention; therefore, GRBs will be entered in the Trigger Catalog before the Burst Catalog. The latency requirements are 1 day for triggers and 3 days for bursts.

Tags: astrophysics, fermi, gamma-ray-bursts, gbm, lat, light-arcs, particle-physics, photons, pulsars, solar-flares, space-science
Organization: National Aeronautics and Space Administration
Effect of simulated microgravity on E. coli K12 MG1655 growth and gene expression

This study demonstrates simulated microgravity effects on E. coli K 12 MG1655 when grown on LB medium supplemented with glycerol. The results imply that E. coli readily reprograms itself to combat the multiple stresses imposed due to microgravity. Under these conditions it survives by upregulating oxidative stress protecting genes and simultaneously down regulating the membrane transporters and synthases to maintain cell homeostasis. In this study a clinostat that mimics microgravity conditions was used to investigate the effects of microgravity on E. coli grown in LB medium supplemented with glycerol to monitor the effects on growth and global gene expression using Affymetrix DNA microarrays.

Tags: bioassay_data_transformation, feature_extraction, grow, hybridization, image_aquisition, labeling, nucleic_acid_extraction, p-gse40648-1, p-gse40648-2, p-gse40648-3, p-gse40648-4, p-gse40648-5, p-gse40648-6, p-gse40648-7, p-gse40648-8, simulated-microgravity, specified_biomaterial_action
Organization: National Aeronautics and Space Administration
LAT 2-year Point Source Catalog Aperture Photometry Lightcurves Flares

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
Genomic Characterization and Virulence Potential of Two Fusarium oxysporum Isolates Cultured from the International Space Station

Two isolates of Fusarium oxysporum, ISS-F3 and ISS-F4, were cultured from the dining table on the International Space Station (ISS). Genomic analyses using EF-1α sequences, presence/absence of effector proteins, k-mer comparisons, and single nucleotide polymorphisms indicate that these two strains are genomically different from 65 known sequenced strains. Functional analysis revealed that ISS-F3/F4 had higher relative abundances of polyketide synthase domains than a non-plant-pathogenic soil isolate, used for biocontrol properties (Fo47), and a clinical isolate (FOSC-3a). Putative secondary metabolite analysis indicates that ISS-F3/F4 may produce yet-unreported polyketides and nonribosomal peptides. While genomic analysis showed that these ISS strains are unlikely to be plant pathogens, a virulence assay using an immunocompromised Caenorhabditis elegans model of fusariosis revealed that they were virulent and may represent opportunistic pathogens in animals, including humans. However, its effects on the health of immunocompromised humans warrant further study.

Tags: sample-collection-nucleic-acid-extraction-nucleic-acid-sequencing-sequence-assembly, spaceflight
Organization: National Aeronautics and Space Administration
Temporal dynamics of the gut microbiota in people sharing a confined environment a 520-day ground-based space simulation MARS500

The MARS500 project the longest ground-based space simulation ever provided us with a unique opportunity to trace the crew microbiota over 520 days of isolated confinement such as that faced by astronauts in real long-term interplanetary space flights and after returning to regular life for a total of 2 years.

Tags: data-transformation, diet, genelab-amplicon-seq-data-processing-protocol, library-construction, nucleic-acid-extraction, nucleic-acid-sequencing, sample-collection, sequence-analysis-data-transformation, time
Organization: National Aeronautics and Space Administration
Rodent Research-3-CASIS: Mouse liver 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, treatment
Organization: National Aeronautics and Space Administration
GBM Accreting Pulsar Histories

For each source we plot the history of pulse frequency and pulsed flux measured using the Fermi Gamma-Ray Burst Monitor (GBM) NaI detectors. For these measurements we use the CTIME data which normally has 0.256 s time bins, and eight energy channels. Our analysis normally uses channels 1 (12-25 keV) and 2 (25-50 keV). The integration interval used varies from source to source, ranging from one to four days. For eclipsing systems each egress to ingress interval is divided into an integral number of equal parts, with no measurement made during the eclipse. The measured frequencies are barycentered. For sources where the binary orbit is known, the frequencies are corrected for the binary motion. The R.M.S. pulsed flux is given in the energy band in which the pulse search was made.

Tags: astrophysics, fermi, gamma-ray-bursts, gbm, lat, light-arcs, particle-physics, photons, pulsars, solar-flares, space-science
Organization: National Aeronautics and Space Administration
Muscle atrophy osteoporosis prevention in hibernating mammals

Physical inactivity decreases the mechanical load on the skeleton which when prolonged leads to losses of muscle strength and bone mass in humans and most mammalian species. Hibernating mammals show no loss in bone mass and less muscle atrophy than would be anticipated over such a prolonged period of physical inactivity. This suggests that diverse hibernating mammals have evolved natural mechanisms that reduce muscle atrophy and conserve bone mass.

Tags: library-construction, nucleic-acid-extraction, nucleic-acid-sequencing, time, treatment-protocol
Organization: National Aeronautics and Space Administration
The development of Drosophila melanogaster during space flight

In prospective human exploration of outer space the need to maintain a species over several generations under changed gravity conditions may arise. This paper reports the analysis of the third generation of fruit fly Drosophila melanogaster obtained during the 44.5-day space flight (Foton-M4 satellite 2014 Russia) followed by the fourth generation on Earth and the fifth generation under conditions of a 12-day space flight (2014 in the Russian Segment of the ISS). The obtained results show that it is possible to obtain the third-fifth generations of a complex multicellular Earth organism under changed gravity conditions (in the cycle weightlessness - Earth - weightlessness) which preserves fertility and normal development. However there were a number of changes in the expression levels and content of cytoskeletal proteins that are the key components of the spindle apparatus and the contractile ring of cells.

Tags: growth-protocol, library-construction, microgravity, nucleic-acid-extraction, nucleic-acid-sequencing, sequence-analysis-data-transformation
Organization: National Aeronautics and Space Administration
Rodent Research-1 (RR1) NASA Validation Flight: Mouse quadriceps 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
Rodent Research-3-CASIS: Mouse liver 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, tmt-isobaric-labeling
Organization: National Aeronautics and Space Administration
Rodent Research-1 (RR1) NASA Validation Flight: Mouse quadriceps 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, 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-sequencing-library-construction, sample-collection, spaceflight, tmt-isobaric-labeling
Organization: National Aeronautics and Space Administration
Transcriptional analysis of spleens from mice preserved with the Rapid Freeze hardware

Data from the NASA Rodent Research-1 (RR-1) mission showed that gene-expression levels in mouse livers are different depending on what tissue preservation protocol is used and that slow freezing is not an effective method for preserving signals in gene-expression data. In response to these and other observations the Rapid Freeze hardware was built for use on the International Space Station. The Rapid Freeze hardware freezes mouse tissues (Glovebox freezer) and whole carcasses (Cryochiller) at rates closely mimicking those attained with immersion in liquid nitrogen. Because this hardware will be used extensively on future rodent research missions it is crucial to understand whether or not it preserves signals in gene expression data in order to maximize the value of these rare and expensive spaceflight experiments. Therefore this study was designed with three goals: 1) To evaluate the temperature profile of the Cryochiller and Glovebox freezer cartridges (Rapid Freeze hardware) over time during mock on-orbit procedures; 2) To determine the freezing profiles of tissues and carcasses using Rapid Freeze hardware at both optimal and sub-optimal temperatures (to mimic on-orbit operations) compared with those frozen in liquid nitrogen (the laboratory gold standard) or frozen in at -80 C (the current standard method); 3) To identify gene expression changes in a) tissues that were frozen via the Glovebox freezer and b) tissues dissected from whole or partial carcasses that were frozen via the Cryochiller versus tissues that were frozen via control methods (liquid nitrogen or -80C slow freeze) to assess how the Rapid Freeze hardware compares with laboratory gold standard practices and our current standard methods.

Tags: dissection-condition-preservation-method-order-of-preservation, treatment-protocol-sample-collection-nucleic-acid-extraction-spike-in-protocol-library-construc
Organization: National Aeronautics and Space Administration