AndreaBozzo/ceres-open-data-index huggingface dataset:
Global Identification of Noncoding RNAs in S. cerevisiae

Genome-wide detection of novel non-coding RNAs in S. cerevisiae by modulating an RNase P pathway through the depletion of a component RPP1. Nearly 400,000 36-mer oligonucleotide probes tiling the entire yeast genome including the mitochondrial chromosome with an average gap of 10 bases between two consecutive probes were synthesized on glass slides using a mask-less array synthesizer. RNA samples for hybridizing to the arrays were extracted from a conditional lethal allele of S. cerevisiae created by placing the RPP1 gene under control of GAL10 promoter. It allowed the expression of RPP1 in galactose-containing culture medium but suppressed its expression in glucose-containing medium. A wild-type isogenic strain was used as a control. Both strains were initially grown in galactose-containing medium and subsequently transferred and resuspended into glucose-containing medium. Eight arrays were hybridized with RNA extracted from the Rpp1-depleted cells at 0 4 7 12 16 21 30h and the control cell at 30h after initial transfer to glucose-containing medium.

Tags: bioassay_data_transformation, data-collection, data-transformation, feature_extraction, labeling, normalization-data-transformation, nucleic-acid-hybridization, p-gse4275-1, p-gse4275-2, p-gse4275-3, rna-extraction, timepoint
Organization: National Aeronautics and Space Administration
Gene expression profiling of human peripheral blood lymphocytes cultured in modeled microgravity

In the present study we analyzed miRNA and mRNA expression profiles in human peripheral blood lymphocytes (PBLs) incubated in microgravity condition simulated by a ground-based Rotating Wall Vessel (RWV) bioreactor. Our results show that 42 miRNAs were differentially expressed in MMG-incubated PBLs compared with 1g-incubated ones. Among these miR-9-5p miR-9-3p miR-155-5p miR-150-3p and miR-378-3p were the most dysregulated. To improve the detection of functional miRNA-mRNA pairs we performed gene expression profiles on the same samples assayed for miRNA profiling and we integrated miRNA and mRNA expression data. The functional classification of miRNA-correlated genes evidenced significant enrichments in the biological processes of immune/inflammatory response signal transduction regulation of response to stress regulation of programmed cell death and regulation of cell proliferation. We identified the correlation between miR-9-3p miR-155-5p miR-150-3p and miR-378-3p expression with that of genes involved in immune/inflammatory response (eg. IFNG and IL17F) apoptosis (eg. PDCD4 and PTEN) and cell proliferation (eg. NKX3-1 and GADD45A). Experimental assays of cell viability and apoptosis induction validated the results obtained by bioinformatics analyses demonstrating that in human PBLs the exposure to reduced gravitational force increases the frequency of apoptosis and decreases cell proliferation. Gene expression profiling was carried out in MMG-incubated PBLs vs. 1g-incubated PBLs on total RNA extracted from the same PBL samples assayed for miRNA profiling. We used the Whole Human Genome Oligo Microarray (Agilent) consisting of ~41.000 (60-mer) oligonucleotide probes which span conserved exons across the transcripts of the targeted full-length genes.

Tags: array-scanning-protocol, hybridization-protocol, individual, labelling-protocol, normalization-data-transformation-protocol, nucleic-acid-extraction-protocol, p-gse57408-1, p-gse57408-10, p-gse57408-11, p-gse57408-12, p-gse57408-13, p-gse57408-14, p-gse57408-15, p-gse57408-2, p-gse57408-3, p-gse57408-4, p-gse57408-5, p-gse57408-6, p-gse57408-7, p-gse57408-8, p-gse57408-9, sample-treatment-protocol, simulated-microgravity
Organization: National Aeronautics and Space Administration
Draft Genome Sequences of Two Fusarium oxysporum Isolates Cultured from Infected Zinnia hybrida Plants Grown on the International Space Station

Draft genome sequences of two Fusarium oxysporum isolates cultured from infected Zinnia hybrida plants grown on the International Space Station

Tags: sample-collection-nucleic-acid-sequencing-sequence-assembly, spaceflight
Organization: National Aeronautics and Space Administration
Transcriptomic analysis of skin from mice subjected to chronic low-dose radiation hindlimb unloading or a combination of both

The purpose of this study was to evaluate transcriptional changes in mouse skin using a ground-based model for spaceflight. This model includes prolonged unloading and low-dose irradiation. Low-dose-rate gamma-radiation was delivered to 6-month old female C57BL/6J mice using 57Co plates (0.04 Gy) to simulate the radiation environment of spaceflight. Anti-orthostatic tail suspension was used to model the unloading fluid shift and physiological stress aspects of the microgravity component of spaceflight. Mice were hindlimb suspended and/or irradiated for 21 days. Mice were euthanized and dorsal skin was collected 7 days following treatment. RNA sequencing data was generated to assess transcriptional changes in these skin samples.

Tags: data-transformation, genelab-rnaseq-data-processing-protocol, hindlimb-unloading, ionizing-radiation, library-construction, nucleic-acid-extraction, nucleic-acid-sequencing, sample-collection, spike-in-protocol, treatment-protocol
Organization: National Aeronautics and Space Administration
Response of Pseudomonas aeruginosa PAO1 to low shear modeled microgravity

Anticipating the risk for infectious disease during space exploration and habitation is a critical factor to ensure safety health and performance of the crewmembers. As a ubiquitous environmental organism that is occasionally part of the human flora Pseudomonas aeruginosa could pose a health hazard for the immuno-compromised astronauts. In order to gain insights in the behavior of P. aeruginosa in spaceflight conditions two spaceflight-analogue culture systems i.e. the rotating wall vessel (RWV) and the random position machine (RPM) were used. Microarray analysis of P. aeruginosa PAO1 grown in the low shear modeled microgravity (LSMMG) environment of the RWV compared to the normal gravity control (NG) revealed a regulatory role for AlgU (RpoE). Specifically P. aeruginosa cultured in LSMMG exhibited increased alginate production and up-regulation of AlgU-controlled transcripts including those encoding stress-related proteins. This study also shows the involvement of Hfq in the LSMMG response consistent with its previously identified role in the Salmonella LSMMG- and spaceflight response. Furthermore cultivation in LSMMG increased heat and oxidative stress resistance and caused a decrease in the culture oxygen transfer rate. Interestingly the global transcriptional response of P. aeruginosa grown in the RPM was similar to that in NG. The possible role of differences in fluid mixing between the RWV and RPM is discussed with the overall collective data favoring the RWV as the optimal model to study the LSMMG-response of suspended cells. This study represents a first step towards the identification of specific virulence mechanisms of P. aeruginosa activated in response to spaceflight-analogue conditions and could direct future research regarding the risk assessment and prevention of Pseudomonas infections for the crew in flight and the general public.

Tags: bioassay_data_transformation, data-transformation, feature_extraction, genelab-microarray-data-processing-protocol, grow, hybridization, image_aquisition, labeling, microgravity-simulation, nucleic_acid_extraction, p-gse16970-1, p-gse16970-2, p-gse16970-3, p-gse16970-4, p-gse16970-5, p-gse16970-6, p-gse16970-7, p-gse16970-8, specified_biomaterial_action
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, altered-gravity, array-scanning-protocol, data-transformation, genelab-microarray-data-processing-protocol, ground-based-facility, growth-protocol, hybridization-protocol, labelling-protocol, nucleic-acid-extraction-protocol, p-gse33801-2, p-gse33801-3, p-gse33801-4, p-gse33801-5, p-gse33801-6, p-gse33801-7, sample-treatment-protocol, sex, temperature
Organization: National Aeronautics and Space Administration
Mouse muscle LC-MSMS upon weightlessness

Upon weightlessness and microgravity deleterious effects on the neurosensory and neurovestibular systems haematological changes and deconditioning of musculoskeletal cardiovascular and cardiopulmonary functions have been reported. In particular loss of muscle mass and strength are triggered by weightlessness in humans during space flights that is similarly observed as a result of physical inactivity conditions and aging on Earth. However skeletal muscle tissue is of paramount importance for health maintenance (e.g. being essential to locomotion heat production and metabolism). To better prevent or eventually treat microgravity-induced muscle atrophy its underlying mechanisms have first to be characterized in detail. Using cutting-edge quantitative proteomics the aim of the present study was therefore to get an in depth view of the molecular regulations triggered by space conditions in skeletal muscles of mice during the 30-day flight of the BION-M1 biosatellite. As muscles differing in their fiber type composition appear to respond differently to microgravity (see above) we characterized here the differential response of the soleus extensor digitorum longus and vastus lateralis muscles.

Tags: absorbed-radiation-dose, data-transformation, extraction, mass-spectrometry, muscle-skeletal, radiation-dosimetry, sample-collection, weightlessness
Organization: National Aeronautics and Space Administration
Plasticity of the human IgM repertoire in response to a long-term spaceflight

Immune dysregulation is among the main adverse outcomes of spaceflight. Despite its crucial role in host protection effects on the human antibody repertoire are unknown. Consequently we examined the IgM repertoire of five cosmonauts 25 days before launch after 64 and 129 days spent on the International Space Station (ISS) and after 1 7 and 30 days of Earth reambulation using high-throughput sequencing. This is the first study of this kind. Our data revealed that the IgM repertoire of cosmonauts was different from the one of control subjects already prior to launch and that 2 out the 5 analyzed cosmonauts presented significant changes of their IgM repertoire during the mission. These modifications persisted up to 30 days after landing likely affected the specificities of IgM binding sites correlated with changes of the V(D)J recombination process in charge of creating functional antibody genes and coincided with a higher stress response. These data confirm that about half of the astronauts who spent six months on the ISS are subjected to immunological changes contribute to explain increased susceptibility to infection reveal individual responses and consequently that personalized approaches should be implemented during future deep-space exploration missions that will endure for an unprecedented amount of time.

Tags: library-construction, nucleic-acid-extraction, nucleic-acid-sequencing, spaceflight, study-subject, time, treatment-protocol
Organization: National Aeronautics and Space Administration
Transcription profiling of rat response to changes in developmental stage - 3 types of tissue 3 gravity conditions 2 developmental conditions

Transcriptional crosstalk between mammary gland liver and adipose tissue Experiment Overall Design: Pregnant and Lactating rats exposed to 3 gravity conditions

Tags: absorbed-radiation-dose, bioassay_data_transformation, developmental-condition, hypergravity, labeling, microgravity, nucleic_acid_extraction, p-g12132-1, p-g12132-2, p-g12132-3, radiation-dosimetry, tissue
Organization: National Aeronautics and Space Administration
Impact of Antiorthostatic Suspension on Mouse response to Tetanus Toxoid and CpG: bone marrow transcriptomic data

These data were generated from mice that were skeletally unloaded using antiorthostatic suspension (AOS). Mice were either subjected to AOS or tail restraint without unloading for two weeks before injection with saline +/- tetanus toxoid +/- Cpg. Mice were unloaded for an additional two weeks before being sacrificed. This set of data focused on bone marrow. The spleen data are available in the GLDS-201.

Tags: animal-treatment, data-transformation, genelab-rnaseq-data-processing-protocol, hindlimb-unloading, nucleic-acid-extraction, nucleic-acid-sequencing, rna-sequencing-library-construction, sample-collection, tetanus-toxoid, vaccine-adjuvant
Organization: National Aeronautics and Space Administration
Global gene expression profiles of cardiac progenitors differentiated from human pluripotent stem cells in 3D culture under simulated microgravity

Methods: RNA-seq libraries were prepared using the Illumina TruSeq RNA kit and the TrueSeq method was employed for mRNA enrichment. The libraries were quantified and samples were multiplexed in each lane of the flowcell. Cluster generation was performed and then sequenced on the Illumina HiSeq1000 system. Reads were mapped on the Human Genome Reference and normalized expression table was generated. Results: Among differentially expressed genes 53 of them were up-regulated and 75 were down-regulated. Conclusions: Data demonstrate increased expression of genes associated with growth development and pro-survival in cardiac progenitors cultured under simulated microgravity compared with those cultured under standard gravity. RNA-sequencing analysis was performed to compare global gene expression profiles of cells at differentiation day 8 under simulated microgravity vs. standard gravity.

Tags: condition, extraction-protocol, library-construction, normalization-data-transformation-protocol, nucleic-acid-sequencing, p-gse84582-1, p-gse84582-2
Organization: National Aeronautics and Space Administration
Sentinel-3B OLCI 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
Streptococcus mutans differential gene expression in response to simulated microgravity

Astronauts have been previously shown to exhibit decreased salivary lysozyme and increased dental calculus and gingival inflammation in response to space flight host factors that could contribute to oral diseases such as caries and periodontitis. However the specific physiological response of caries-causing bacteria such as Streptococcus mutans to space flight and/or ground-based simulated microgravity has not been extensively investigated. In this study High Aspect Ratio Vessel (HARV) S. mutans simulated microgravity and normal gravity cultures were assessed for changes in metabolite and transcriptome profiles H2O2 resistance and competence in sucrose-containing biofilm media. Stationary phase S. mutans simulated microgravity cultures displayed increased killing by H2O2 compared to normal gravity control cultures but competence was not affected. RNA-seq analysis revealed that expression of 153 genes was up-regulated >= 2-fold and 94 genes down-regulated >= 2-fold during simulated microgravity HARV growth. These included a number of genes located on extrachromosomal elements as well as genes involved in carbohydrate metabolism translation and stress responses. Collectively these results suggest that growth under microgravity analog conditions promotes changes in S. mutans gene expression and physiology that may translate to an altered cariogenic potential of this organism during space flight missions. Overall design: Differential gene expression was compared between RNA from S. mutans grown in normal gravity HARVs (n=3 independent cultures) and RNA from S. mutans grown in simulated microgravity HARVs (n=3 independent cultures)

Tags: library-construction, nucleic-acid-extraction, nucleic-acid-sequencing, sample-collection, sequence-analysis-data-transformation, weightlessness-simulation
Organization: National Aeronautics and Space Administration
Gene-expression profiling of Saccharomyces cerevisiae irradiated by high-LET radiations

Ionizing radiations are categorized by linear energy transfer (LET) into low-LET and high-LET. High-LET is considered to have a higher relative biological effectiveness (RBE) than low-LET radiations. However the details of the effects have not been clearly determined. The aim of this study was to characterize the difference between high-LET and low LET radiations. The global effects of the three types of high-LET radiations (fast neutron heavy ion (C) and thermal neutron) were compared with the low-LET radiation (gamma ray) using yeast DNA microarrays. Highly induced genes by the three types of high-LET radiations were those genes related to oxidative stress. Oxidative stress was one of the common factors associated with the four types of radiations. Oxidative stress induced by high-LET radiations may be more serious than that induced by gamma rays. Additionally genes related to protein synthesis and the ubiquitin and proteasome system were detected. This suggests that more protein damages can be induced by high-LET radiation that denatures the proteins in yeast cells. The genes specifically altered by each type of high-LET radiation were also studied. Overall design: This series contains 4 kinds of irradiation-induced gene expression profiles. Triplicates hybridization was done in each irradiation exposure and each array have high and low power scanned data respectively. All biological samples were collected independently.

Tags: data-collection, data-transformation, growth-and-treatment-protocol, labeling, normalization-data-transformation, nucleic-acid-hybridization, radiation-ionzing, rna-extraction
Organization: National Aeronautics and Space Administration
Molecular mechanism of flocculation self-recognition in yeast and its role in mating and survival

Saccharomyces cerevisiae flocculation occurs when fermentable sugars are limiting and is therefore considered as a way to enhance the survival chance of Flo-expressing yeast cells. In this paper the role of Flo1p in mating was demonstrated by showing that the mating efficiency which contributes to the increased survival rate as well by generating genetic variability is increased when cells flocculate. This was revealed by liquid growth experiments in a low shear environment and differential transcriptome analysis of FLO1 expressing cells compared to the non-flocculent wild-type cells. The results show that a floc provides a uniquely organized multicellular ultrastructure that provides a suitable microenvironment to induce and perform cell conjugation. S. cerevisiae strains BY4742 WT BY4742::FLO8 and BY4742 [FLO1] were grown in microgravity and 1-g. A transcriptomic analysis was performed and the transcriptome data were integrated with the high quality protein-protein interaction networks. The identified high score sub-networks (qvalue < 0.001) were considered and further evaluated concerning their GO enrichment using a hypogeometric test. The data were from the Ying B-1 experiment.

Tags: array-scanning-protocol, data-transformation, genelab-microarray-data-processing-protocol, genotype, growth-protocol, hybridization-protocol, labelling-protocol, nucleic-acid-extraction-protocol, p-gse64468-2, p-gse64468-3, p-gse64468-4, p-gse64468-5, p-gse64468-6, p-gse64468-7, sample-treatment-protocol, spaceflight
Organization: National Aeronautics and Space Administration
Insulated-Gate Bipolar Transistor (IGBT) Accelerated Aging

Preliminary data from thermal overstress accelerated aging using the aging and characterization system. The data set contains aging data from 6 devices, one device aged with DC gate bias and the rest aged with a squared signal gate bias. Several variables are recorded and, in some cases, high-speed measurements of gate voltage, collector-emitter voltage, and collector current are available. The data set is provided by the NASA Prognostics Center of Excellence (PCoE).

Tags: accelerated-aging, degradation, igbt, insulated-gate-bipolar-transistor, phm, prognostics, semiconductor, transistor
Organization: National Aeronautics and Space Administration