AndreaBozzo/ceres-open-data-index huggingface dataset:
Effect of a 91 day long stay in weightlessness on the International Space Station on mouse skin physiology

Comparative gene expression in skin between mice maintained in microgravity (0g) and normogravity (1g) environment. Six male C57Bl/J10 mice were housed for 91 days in the specially designed Mouse Drawer System in weightlessness aboard the International Space Station. Three wild-type mice (WT) and three transgenic mice overexpressing the osteogneic factor PTN/OSF1 under the control of the human bone specific ostecalcin promoter (Tg) were used in the experiment. During the 3-month stay on the ISS 3 mice unfortunately died leaving 2 Tg and 1 WT. MDS tissue sharing program allowed several teams to study various tissues from these mice. Our aim was to investigate the effect of such a long period of microgravity on skin physiology by morphological biochemical and genomewide analyses by comparison to similar mice on ground. Gene expression in the skin of 3 space mice and of 3 ground mice was analyzed by microarray. As this unique experiment performed on 3 mice limits the power of statistical analyis as the transgene PTN/OSF1 was not overexpressed in skin and as a pair wise Pearson  s correlation rates between the individual levels of expressed transcripts in the WT and the Tg mice were not significantly different from each other in one experimental group (space or ground) data from the 3 mice were combined to compare results from the space an ground groups.

Tags: array-scanning-and-feature-extraction-protocol, data-transformation, genelab-microarray-data-processing-protocol, genotype, nucleic-acid-extraction-protocol, nucleic-acid-hybridization-to-array-protocol, nucleic-acid-labeling-protocol, p-mtab-40820, p-mtab-40821, p-mtab-40822, p-mtab-40823, p-mtab-40824, sample-collection-protocol, spaceflight, treatment-protocol
Organization: National Aeronautics and Space Administration
Transcription profiling of mouse osteoblasts under static vs simulated microgravity

The total RNA was extracted from 2T3 pre-osteoblast cells exposed to static or simulated microgravity (Rotating Wall Vessel) conditions. The RNA was then sent to Affymetrix microarray core facility at Baylor College of Medicine (Houston TX) for microarray analysis.

Tags: data-transformation, genelab-microarray-data-processing-protocol, growth-protocol, microgravity-simulation, nucleic-acid-hybridization, rna-extraction, treatment-protocol
Organization: National Aeronautics and Space Administration
Sentinel-3B OLCI Regional Mapped Inland Waters (ILW) Data, version 4

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

Tags: aquatic-sciences, bacteria-archaea, biological-classification, biosphere, coastal-processes, earth-science, earth-science-services, ecosystems, environmental-advisories, environmental-governance-management, human-dimensions, hydrological-advisories, marine-environment-monitoring, ocean-optics, oceans, surface-water, terrestrial-hydrosphere, water-quality-water-chemistry
Organization: National Aeronautics and Space Administration
Environmental and simulation facility conditions can modulate a behavioral-driven altered gravity response of Drosophila imagoes transcriptome

Genome-wide transcriptional profiling shows that reducing gravity levels in the International Space Station (ISS) causes important alterations in Drosophila gene expression. However simulation experiments on ground without space constraints show weaker effects than space environment. A global and integrative analysis using the gene expression dynamics inspector (GEDI) self-organizing maps reveals a subtle response of the transcriptome using different populations and microgravity and hypergravity simulation devices. These results suggest that in addition to behavioural responses that can be detected also at the gene expression level the transcriptome is finely tuned to normal gravity. The alteration of this constant parameter on Earth can have effects on gene expression that depends both on the environmental conditions and the ground based facility used to compensate the gravity vector. Alternative and commons effects of mechanical facilities like the Random Positioning Machine and a centrifuge and strong magnetic field ones like a cryogenically cooled superconductive magnet are discussed. We compare the effects over the gene expression profile of different gender/age Drosophila imagoes in 3-4 days-long experiments under altered gravity conditions into three GBF (Ground Based Facilities for micro/hyper- gravity simulation) using whole genome microarray platforms. Descriptions of different GBFs (treatments): LDC means Large Diameter Centrifuge. Samples can be placed under three conditions: inside LDC (at certain g level) at the LDC rotational control and at external 1g control (outside the LDC). RPM means Random Positioning Machine. Samples can be placed under two conditions: inside RPM (at nearly 0g Microgravity level) and at external 1g control (outside the RPM). At the magnet means INSIDE the Magnetic levitator (another GBF). Samples can be placed under four conditions: inside Magnet 0g* (at microgravity with magnetic field) inside Magnet at 1g* (internal control with magnetic field) or inside the magnet 2g* (at hypergravity with magnetic field) and at external 1g control (outside the magnet)

Tags: age, array-scanning-protocol, growth-protocol, hybridization-protocol, hypergravity, labelling-protocol, normalization-data-transformation-protocol, nucleic-acid-extraction-protocol, p-gse33801-1, p-gse33801-2, p-gse33801-3, p-gse33801-4, p-gse33801-5, p-gse33801-6, p-gse33801-7, sample-treatment-protocol, sex, simulated-microgravity, temperature
Organization: National Aeronautics and Space Administration
Exposure to ionizing radiation induced persistent gene expression changes in mouse mammary gland

Six to eight week old female C57BL/6J mice were exposed to 2 Gy of whole body  xce xb3 radiation and mammary glands were surgically removed 2-month after radiation. RNA was isolated and microarray hybridization performed for gene expression analysis. 5 samples were analyzed: 2 controls at 2 months 1 2 Gy at 2 months and 2 7 Gy at 2 months

Tags: array-scanning-protocol, dose, growth-protocol, hybridization-protocol, ionizing-radiation, labelling-protocol, normalization-data-transformation-protocol, nucleic-acid-extraction-protocol, p-gse57196-1, p-gse57196-2, p-gse57196-3, p-gse57196-4, p-gse57196-5, p-gse57196-6, p-gse57196-7, sample-treatment-protocol
Organization: National Aeronautics and Space Administration
International Space Station - Microbial Observatory of Pathogenic Virus Bacteria and Fungi project

This study investigated the interplay between the microbial community of the International Space Station and its crew. Environmental samples were collected from 8 habitable locations around the ISS. The microbial composition was measured using shotgun metagenomic sequencing and procesed using the Livermore Metagenomics Analysis Toolkit.

Tags: library-construction, nucleic-acid-extraction, nucleic-acid-sequencing, sample-collection, sample-location, sequence-assembly, spaceflight, time, treatment
Organization: National Aeronautics and Space Administration
Global gene expression analysis highlights microgravity sensitive key genes in longissimus dorsi and tongue of 30 days space-flown mice

Microgravity as well as chronic muscle disuse are two causes of low back pain originated at least in part from paraspinal muscle deconditioning. At present no study investigated the complexity of the molecular changes in human or mouse paraspinal muscles exposed to microgravity. The aim of this study was to evaluate longissimus dorsi and tongue (as a new potential in-flight negative control) adaptation to microgravity at global gene expression level. C57BL/N6 male mice were flown aboard the BION-M1 biosatellite for 30 days (BF) or housed in a replicate flight habitat on ground (BG). Global gene expression analysis identified 89 transcripts differentially regulated in longissimus dorsi of BF vs. BG mice (False Discovery Rrate < 0,05 and fold change < -2 and > +2) while only a small number of genes were found differentially regulated in tongue muscle ( BF vs. BG = 27 genes). 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
NASA Standards and and Technical Assistance Resource Tool

The NASA Technical Standards Program provides access to NASA developed standards and handbooks. The NASA Standards and Technical Assistance Resource Tool, or START, is a Web tool sponsored by the NASA Technical Standards Program. The idea is to make it simpler for technical people to access great NASA technical information quickly and conveniently.

Tags: climate, earth-science, institutional, journal-papers, operations, space-science, technical-reports
Organization: National Aeronautics and Space Administration
Human skin fibroblast mitochondrial depletion 0.5 Gy alpha-particle

Mitochondrial DNA-depleted human skin fibroblasts (HSF rho0) with suppressed oxidative phosphorylation were characterized by significant changes in the expression of 2100 nuclear genes encoding numerous protein classes in NF-kappaB and STAT3 signaling pathways and by decreased activity of the mitochondrial death pathway compared to the parent rho+ HSF. In contrast the extrinsic TRAIL/TRAIL-Receptor-mediated death pathway remained highly active and exogenous TRAIL induced higher levels of apoptosis in rho0 cells compared to rho+ HSF. Global gene expression analysis using microarray and quantitative RT-PCR demonstrated that expression levels of many growth factors and their adaptor proteins (FGF13 HGF IGFBP4 IGFBP6 IGFL2) cytokines (IL6 IL17B IL18 IL19 IL28B) and cytokine receptors (IL1R1 IL21R IL31RA) were substantially decreased after mitochondrial depletion. Some of these genes were targets of NF-kappaB and STAT3 and their protein products could regulate the STAT3 signaling pathway. Alpha-irradiation induced expression of several NF-kappaB/STAT3 target genes including IL1A IL1B IL6 PTGS2/COX2 and MMP12 in rho+ HSF but this response was substantially decreased in rho0 HSF. Suppression of the IKK-NF-kappaB pathway by the small molecular inhibitor BMS-345541 and of the JAK2-STAT3 pathway by AG490 dramatically increased TRAIL-induced apoptosis in the control and irradiated rho+ HSF. Inhibitory antibodies against IL6 the main activator of JAK2-STAT3 pathway added into the cell media also increased TRAIL-induced apoptosis in rho+ HSF. However NF-kappaB activation was partially lost in mitochondrial DNA-depleted HSF resulting in downregulation of the basal or radiation-induced expression of numerous NF-kappaB targets further suppressing IL6-JAK2-STAT3 that in concert with NF-kappaB regulated protection against TRAIL-induced apoptosis. There are 12 total samples 3 biological replicates each of HSF rho+ and rho0 cells that were not irradiated (control=C) or irradiated (alpha=A). Cells were harvested at 4 hours after treatment.

Tags: bioassay_data_transformation, dose, feature_extraction, grow, hybridization, image_aquisition, ionizing-radiation, labeling, mitochondrial-status, nucleic_acid_extraction, p-gse24945-1, p-gse24945-2, p-gse24945-3, p-gse24945-4, p-gse24945-5, p-gse24945-6, p-gse24945-7, p-gse24945-8, specified_biomaterial_action
Organization: National Aeronautics and Space Administration
LAT Bright Source List

The Fermi Gamma-ray Space Telescope (Fermi) Large Area Telescope (LAT) is a successor to EGRET, with greatly improved sensitivity, resolution, and energy range. This web page presents the first full catalog of LAT sources, based on the first eleven months of survey data. For a full explanation about the catalog and its construction see the LAT 1-year Catalog Paper.

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
Merged Sentinel-3A and Sentinel-3B OLCI Regional Mapped Inland Waters (ILW) Data, version 4

The Inland Waters dataset (ILW) provides data for lakes and other water bodies across the contiguous United States (CONUS) and Alaska. ILW significantly reduces the processing effort required by end users and is a standardized community resource for lake and reservoir algorithm development and performance assessment.The data is provided for 15,450 CONUS waterbodies with a size of at least one 300 m pixel and over 2,300 resolvable lakes with sizes greater than three 300 m pixels. Alaska has 5,874 lakes resolvable lakes. ILW is a times series containing 10 years of MERIS (2002-2012) and OLCI from both Sentinel-3a (2016-present) and Sentinel-3b (2018-present).

Tags: aquatic-sciences, bacteria-archaea, biological-classification, biosphere, coastal-processes, earth-science, earth-science-services, ecosystems, environmental-advisories, environmental-governance-management, human-dimensions, hydrological-advisories, marine-environment-monitoring, ocean-optics, oceans, surface-water, terrestrial-hydrosphere, water-quality-water-chemistry
Organization: National Aeronautics and Space Administration
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, data-transformation, feature_extraction, genelab-microarray-data-processing-protocol, hindlimb-unloading, hybridization, p-affy-6, treatment, treatment-protocol
Organization: National Aeronautics and Space Administration
Analysis of dust samples from the Russian part of the ISS

Our study focuses on the hardiest microorganisms inhabiting the ISS in order to assess their diversity and capabilities to resist certain stresses. We specifically selected dust samples from the Russian modules that were obtained 8-10 years ago and stored since then under sealed conditions on Earth. Targeting long-time survivors and spore-forming microorganisms we assessed consequently the cultivable microbial community of these samples in order to obtain model microbial strains that could help to analyze specific adaptation towards environmental stresses such as desiccation and lack of nutrients. In this study we analyzed these microorganisms with respect to their resistance towards thermal stress and exposure to clinically relevant antibiotics. In addition we assessed the bacterial and archaeal community via molecular methods (NGS sequencing) and compared our new data with the previously derived information from the ISS microbiome.

Tags: environmental-stress, library-construction, microgravity, nucleic-acid-extraction, nucleic-acid-sequencing, sample-collection, sequence-analysis-data-transformation
Organization: National Aeronautics and Space Administration
Transcriptomic analysis of dorsal skin from mice flown on the MHU-2 mission

The JAXA MHU-2 mission had two objectives: 1) To increase understanding of effects of spaceflight on the gut environment (microbiota and metabolites) and immune system using multi-omics based analysis; 2) To evaluate whether fructo-oligosaccharides added to the diet as prebiotics improve the gut environment and immune function during spaceflight. Twelve 16-18 week old male C57BL/6J mice were singly housed in the JAXA Habitat Cage Units (HCUs) on the ISS for 30 days. Six flight mice were housed in microgravity while six were exposed to simulated 1g by centrifugation. These two flight groups were further divided in half so that three mice in each group received standard JAXA chow while the other three were fed chow supplemented with fructooligosaccharides (FOS). Mice were returned live and euthanized and dissected <1 day after splashdown. Ground controls (n=6) were asynchronous and housed in HCUs. Vivarium controls (n=6) were asynchronous and housed in standard habitats. Three ground control and three vivarium animals received standard chow while the other three each ground control and vivarium animals received FOS-supplemented chow. Ground and vivarium samples were dissected by a separate dissection team than flight samples. Dorsal skin was dissected 30 minutes after euthanasia and snap frozen in liquid nitrogen. Total RNA was extracted and sequenced at a target depth of 60 M clusters per sample (ribodepleted paired end 150). Study Factor Levels: 1)Spaceflight ug Std. Chow: 3; 2)Spaceflight ug FOS: 3; 3) Spaceflight Artificial 1g Std. Chow: 3; 4)Spaceflight Artificial 1g FOS: 3; 5)Ground 1g Std. Chow: 3; 6)Ground 1g FOS: 3; 7)Vivarium 1g Std. Chow: 3; 8)Vivarium 1g FOS: 3.

Tags: altered-gravity, animal-husbandry, data-transformation, diet, genelab-rnaseq-data-processing-protocol, library-construction, mouse-habitation, nucleic-acid-extraction, nucleic-acid-sequencing, sample-collection, spaceflight, spike-in-protocol
Organization: National Aeronautics and Space Administration
Rodent Research-1 (RR1) National Lab Validation Flight: Mouse liver transcriptomic proteomic and epigenomic data

The Rodent Reasearch-1 National Lab (RR-1 CASIS) experiment was performed to study the effect of microgravity on muscle wasting. RNA DNA and protein were purified from RR-1 CASIS (the Center for the Advancement of Science in Space) liver samples. Groups included: Flight (FLT) dissected on-orbit (21 or 22 days after launch); age-matched Ground Controls (GC); and Basal Controls (BC euthanized at time of launch). RNA-Seq whole genome BS-Seq (bisulfite sequencing) and proteomic expression profiling were performed.

Tags: animal-husbandry, data-transformation, dna-sequencing-library-construction, extraction, genelab-rnaseq-data-processing-protocol, labeling, library-construction, 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
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: data-transformation, genelab-rnaseq-data-processing-protocol, generation, growth-protocol, library-construction, nucleic-acid-extraction, nucleic-acid-sequencing, sequence-analysis-data-transformation, spaceflight, time
Organization: National Aeronautics and Space Administration
Methylome Analysis of Arabidopsis Seedlings Exposed to Microgravity

DNA methylation is a very important kind of epigenetic modification and participates in many biological functions. Although many previous studies have addressed various plant species the study of global DNA methylation pattern in response to microgravity conditions has been quite limited. In this report we map the changes in Arabidopsis genome methylation patterns - at the single-base resolution - associated with microgravity conditions on board of the spacecraft SJ-10 mission in China.

Tags: growth-protocol, library-construction, nucleic-acid-extraction, nucleic-acid-sequencing, sequence-analysis-data-transformation, spaceflight, treatment-protocol
Organization: National Aeronautics and Space Administration
Spaceflight Modulates Gene Expression in Astronauts

Astronauts are exposed to a unique combination of stressors during spaceflight, which leads to alterations in their physiology and potentially increases their susceptibility to infectious pathogens. Here we report the first microarray evaluation of any astronaut tissue sample, specifically whole blood, before and after spaceflight using an array comprising 234 well-characterized stress response genes. Differentially regulated genes included those important for DNA repair, oxidative stress, and protein folding/degradation. Microarrays comprising 234 well characterized stress-related genes were used to profile transcriptomic changes in six astronauts before and after short-duration spaceflight. Blood samples were collected for analysis from each eastronaut 10 days prior and 2-3 hours after return from spaceflight. Data submitted for platform GPL140 contain genes that have been pre-filtered by the analytical software to remove values of low certainty, resulting in missing values for some samples. Unfortunately, these original data are no longer available due to physical damage at Tulane University during hurricane Katrina, but the processed values were retained in redundant locations and these are submitted for upload to GEO.

Tags: p-gse47126-3-nucleic-acid-extraction-protocol-labelling-protocol-hybridization-protocol-array-s, p-gse47126-3-p-gse47126-5-p-gse47126-6-p-gse47126-7-p-gse47126-8-p-gse47126-1-p-gse47126-2, spaceflight-sex-study-subject-time
Organization: National Aeronautics and Space Administration