AndreaBozzo/ceres-open-data-index huggingface dataset:
Selecting for Chlamydomonas reinhardtii fitness in the KSC Veggie Unit

The Space Algae Experiment Verification Test completed a competitive growth selection on mutagenized microalgae in a series of batch cultures that were passaged for three growth cycles. The experiment was conducted with ground control conditions similar to those actually used in spaceflight. Cultures were limited in growth rate due to gas permeable membranes to provide oxygen and carbon dioxide exchange and a lack of agitation to mix the cells throughout the liquid media. Two strains were grown and three biological replicates were completed for each strain. Specific variables (factors) tested were: 1) The effect of UVC mutagenesis was tested by sampling the algae cultures prior to mutagenesis. 2) The sensitivity of different strains was tested by conducting the experiment with a wild-type and cell wall mutant (cw15) strain. 3) The effect of competitive growth was tested by sampling each biological replicate experiment at the end of each growth cycle. 4) The effect of live culture storage in the dark was tested by sampling each growth cycle twice. At the time of passage a sample of cells was pelleted and frozen. The cultures were then stored in the dark in a Cargo Transport Bag (CTB) to simulate storage on the ISS and return of cultures. This factor tested whether cultures could be stored alive in the dark or if samples needed to be fixed at the time of passage in order to get an accurate representation of the genetic variation in each cycle of growth. Paired-end whole genome sequencing was completed for 38 samples: 2 strains pre mutagenesis and 2 strains X 3 biological replicates X 3 growth cycles X 2 storage conditions.

Tags: growth-cycle, growth-protocol, library-construction, nucleic-acid-extraction, nucleic-acid-sequencing, sample-collection, sample-storage, strain, uv-mutagenesis
Organization: National Aeronautics and Space Administration
A study of alterations in DNA epigenetic modifications (5mC and 5hmC) influenced by simulated microgravity in human lymphoblastoid cells

Here in this study we systematically examined the patterns of DNA methylation and hydroxy-methylation with its functional implications in gene regulation for the cultured TK6 lymphoblastoid cells upon exposure to micro-gravity conditions. The results reported here indicate that simulated microgravity alters methylation patterns in a limited way and subsequently the expression of genes involved in stress response like ATF3 FBXO17 MAP3K13 and VCL in TK6 cells. Overall design: Examination of RNA-seq with 2 replicates each for 1 cell type

Tags: nucleic-acid-extraction-library-construction-nucleic-acid-sequencing-sequence-analysis-data-tra, weightlessness-simulation
Organization: National Aeronautics and Space Administration
Adaptive changes in the vestibular system of land snail to a 30-day spaceflight and readaptation on return to Earth

The vestibular system receives a permanent influence from gravity and reflexively controls equilibrium. If we assume gravity has remained constant during the species   evolution will its sensory system adapt to abrupt loss of that force? We address this question in the land snail Helix lucorum exposed to 30 days of near weightlessness aboard the Bion-M1 satellite and studied geotactic behavior of postflight snails differential gene expressions in statocyst transcriptome and electrophysiological responses of mechanoreceptors to applied tilts. Each approach revealed plastic changes in the snail  s vestibular system assumed in response to spaceflight. Absence of light during the mission also affected statocyst physiology as revealed by comparison to dark-conditioned control groups. Readaptation to normal tilt responses occurred at ~20 h following return to Earth. Despite the permanence of gravity the snail responded in a compensatory manner to its loss and readapted once gravity was restored.

Tags: animal-housing, food-deprivation, library-construction, light-cycle, nucleic-acid-extraction, nucleic-acid-sequencing, sample-collection, spaceflight, water-deprivation
Organization: National Aeronautics and Space Administration
Insulin resistance induced by physical inactivity is associated with multiple transcriptional changes in skeletal muscle in young men

Physical inactivity is a risk factor for insulin resistance. We examined the effect of nine days of bed rest on basal and insulin stimulated expression of genes potentially involved in insulin action by applying hypothesis-generating microarray in parallel with candidate gene real-time PCR approaches in 20 healthy, young men. Furthermore, we investigated whether bed rest affected DNA methylation in the promoter region of the peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PPARGC1A) gene. Subjects were re-examined after four weeks of retraining. Findings: Bed rest induced insulin resistance and altered the expression of more than 4,500 genes. These changes were only partly normalized after four weeks of retraining. Pathway analyses revealed significant down-regulation of 34 pathways, predominantly those of genes associated with mitochondrial function including PPARGC1A. Despite induction of insulin resistance, bed rest resulted in a paradoxically increased response to acute insulin in the general expression of genes, particularly those involved in inflammation and endoplasmatic reticulum (ER) stress. Furthermore, bed rest changed gene expressions of several insulin resistance and diabetes candidate genes. We also observed a trend toward increased PPARGC1A DNA methylation after bed rest. Conclusions: Impaired expression of PPARGC1A and other genes involved in mitochondrial function as well as a paradoxically increased response to insulin of genes involved in inflammation and ER stress may contribute to the development of insulin resistance induced by bed rest. Lack of complete normalization of changes after four weeks of exercise retraining underscores the importance of maintaining a minimum of daily physical activity.

Tags: bed-rest-time-study-subject-treatment, treatment-protocol-rna-extraction-labeling-nucleic-acid-hybridization-data-collection
Organization: National Aeronautics and Space Administration
Transcriptional analysis of soleus 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 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
IMR90 bystander experiment 0.5 Gy alpha particle

The existence of a radiation bystander effect in which non-irradiated cells respond to signals from irradiated cells is well established. It raises concerns for the interpretation of risks from exposure to low doses of ionizing radiation. Sparse data exists about the bystander signaling mechanisms and the ability to transmit damaging effects both spatially and temporally. To understand early signaling and cellular changes in bystanders we have measured global gene expression 30 minutes after direct and bystander exposure to alpha particle in primary human lung fibroblasts. Gene ontology and pathway analyses suggested that the earliest measured changes at 30 minutes after treatment are in cell structure motility and adhesion categories and a significant number of genes belong to the category of inflammation and cell-to-cell communication. We investigated time course gene expression profiles of matrix metalloproteinases 1 and 3 (MMP1 and MMP3) chemokine ligands 2 3 and 5 (CXCL2 CXCL3 and CXCL5) interleukins 1a 1b 6 and 33 (IL1A IL1B IL6 and IL33) growth differentiation factor 15 (GDF15) and superoxide dismutase2 (SOD2) by real time quantitative PCR. These encode proteins involved in cellular signaling via the NFkappaB pathway and time course of mRNA levels revealed an increased response at 30 minutes after irradiation followed by another wave at 4 to 6 hours. We also investigated protein modifications in the AKT-GSK-3 signaling pathway and found that in irradiated cells AKT and GSK3beta are hyper-phosphorylated at 30 minutes and this effect is maintained until 4 hours after exposure. In bystanders there is a similar response with a delay of 30 minutes. In irradiated cells inactivated GSK3beta led to decreased phosphorylation of beta-catenin. Our results are the first to show that the radiation induced bystander signal can induce a widespread gene expression response as early as 30 minutes after exposure and that these changes are accompanied by protein modification of signaling modules such as AKT and GSK3beta. There are 12 total samples 4 corresponding biological replicates of IMR90 cells that were not irradiated (control=C) irradiated (alpha=A) and bystander (B) cells were harvested 0.5 hr after treatment

Tags: bioassay_data_transformation, bystander, dose, feature_extraction, grow, hybridization, image_aquisition, ionizing-radiation, labeling, nucleic_acid_extraction, p-gse18760-1, p-gse18760-2, p-gse18760-3, p-gse18760-4, p-gse18760-5, p-gse18760-6, p-gse18760-7, p-gse18760-8, specified_biomaterial_action
Organization: National Aeronautics and Space Administration
"Molecular Transducers of Human Skeletal Muscle Remodeling under Different Loading States"

"The annotation of the Affymetrix HTA 2.0 array was updated to optimise the detection of RNA in human skeletal muscle biopsy samples by removing invalid and low signal-high-variance probes (as for CDF GPL24047). The probes were then summarized into groups (probe-sets) reflecting either an ensembl full transcript identifier (FL-ENST, GPL24047) or just the probes targeting the 3' UTR or the 5' UTR of that particular ENST. Therefore, 3 different CDF were used to process the HTA 2.0 arrays in this study. Note that each CEL file was GC adjusted using APT while our custom CDF pipeline removes any probe that has >80% or <20% GC content (~50,000). The analysis was carried out only on the pairs of probe-sets i.e. FL-ENST vs 3'UTR or FL-ENST vs 5'UTR or 3'UTR vs 5'UTR. Dynamic muscle loading alters tissue phenotype reflecting altered metabolic and functional demands. In humans, heterogeneous adaptation to loading complicates identification of the underpinning molecular regulators. We present a within-person analysis strategy that reduced heterogeneity for changes in muscle mass by ~40% and employed a genome-wide transcriptome method that modeled each mRNA from coding exons and 3’/5’ untranslated (UTR) regions. Our strategy detected ~3-4 times more regulated genes than similarly sized studies, including substantial UTR-selective regulation that other methods would not detect. We discovered a core of 141 genes correlated to muscle growth validated from newly analyzed independent samples (n=100). Further validating these identified genes, via RNAi in primary muscle cells, we demonstrate that members of the core genes were regulators of protein synthesis e.g. Molecular Transducers of Physical Activity in Humans MoTrPAC. Employing proteome-constrained networks and pathway analysis revealed notable relationships with the molecular characteristics of human muscle aging and insulin sensitivity, as well as potential drug-therapies."

Tags: hindlimb-unloading-age-study-subject-time, rna-extraction-labeling-nucleic-acid-hybridization-data-collection-treatment-protocol-sample-co
Organization: National Aeronautics and Space Administration
Effect of electromagnetic fields on the chondrogenic differentiation under microgravity conditions

A combination therapy of electromagnetic fields (EMF) and simulated microgravity (SMG) has not been examined in regenerative medicine of cartilage. In the present study a bioreactor system using extremely low-frequency EMF and SMG was applied during the chondrogenic differentiation of human mesenchymal stem cells (hMSCs). It was hypothesized that a beneficial effect of EMF regarding chondrogenesis (COL2A) could be combined with an avoiding effect of SMG regarding hypertrophy (COLXA1) of cartilage. Pellet cultures of hMSCs formed cartilaginous tissue under the addition of growth factors (FGF; TGF-beta3). Pure SMG reduced COLXA1 expression but also COL2A expression of hMSCs. Pure EMF showed no gene expression changes of hMSCs during chondrogenic differentiation. Combining EMF/SMG resulted in a re-increase of COL2A but did not reach control levels. The COL2A to COLXA1 ratio of combined EMF/SMG was not significantly different from control levels. The combination therapy of EMF/SMG did not significantly improve the chondrogenic potential of hMSCs. chondrogenic differentiation electromagnetic stimulation-control 1 timepoint with/without stimulation.

Tags: array-scanning-protocol, data-transformation, electromagnetic-fields, genelab-microarray-data-processing-protocol, growth-protocol, hybridization-protocol, labelling-protocol, normalization-data-transformation-protocol, nucleic-acid-extraction-protocol, p-gse57298-1, p-gse57298-2, p-gse57298-3, p-gse57298-4, p-gse57298-5, p-gse57298-6, p-gse57298-7, sample-treatment-protocol
Organization: National Aeronautics and Space Administration
Lunar Orbiter Photo Gallery

The Lunar Orbiter Photo Gallery is an extensive collection of over 2,600 high- and moderate-resolution photographs produced by all five of the Lunar Orbiter missions. These photographs were taken in 1966 and 1967 to survey possible lunar landing sites and provide baseline imagery for geologic analysis of the lunar surface. The images were used to select the Apollo landing sites and to produce many of our existing lunar geologic maps. This photo gallery is the web's most comprehensive collection of Lunar Orbiter photography and supporting documents.

Tags: circulation, geodata, jupiter, lunar-science, modeling, space-science
Organization: National Aeronautics and Space Administration
Land Ice: Greenland & Antarctic ice mass anomaly

Data from NASA's Grace satellites show that the land ice sheets in both Antarctica and Greenland are losing mass. The continent of Antarctica (left chart) has been losing more than 100 cubic kilometers (24 cubic miles) of ice per year since 2002.

Tags: apps, arctic-sea-ice, carbon-dioxide, climate, electricity, ephemerides, geodetics, land-ice, news, radar, waves
Organization: National Aeronautics and Space Administration
Expression data from SPHINX (SPaceflight of Huvec: an INtegrated eXperiment)

Changes in the physical environment modulate cell responses and may lead to the impairment or even failure of tissue function as a result of mechanotransduction processes. It has been suggested that this situation occurs in some age-related diseases and some pathological conditions observed in space such as cardiovascular deconditioning bone loss muscle atrophy and impaired immune responses. All of these are associated with endothelial dysfunction but the precise mechanism is still unclear. We used the microarray approach to obtain insights into the mechanism responsible for endothelial dysfunction by taking advantage of the challenging environment of gravitational unloading onboard the International Space Station. The effects of gravitational unloading on HUVEC gene expression were investigated by means of cDNA microarray analyses of six randomly chosen samples (three for each of the two conditions of spaceflight and 1g) using Affymetrix Gene Human 1.0 ST Arrays

Tags: bioassay_data_transformation, feature_extraction, grow, hybridization, image_aquisition, labeling, microgravity, nucleic_acid_extraction, p-gse43582-1, p-gse43582-2, p-gse43582-3, p-gse43582-4, p-gse43582-5, p-gse43582-6, p-gse43582-7, p-gse43582-8, spaceflight, specified_biomaterial_action
Organization: National Aeronautics and Space Administration
BASE-A space experiment with Rhodospirillum rubrum S1H

R. rubrum S1H inoculated on solid minimal media was sent to the ISS in September 2006 (BASE-A experiment). After 10 days flight R. rubrum cultures returned back to Earth. These cultures were then subjected to both transcriptomic and proteomic analysis and compared with the corresponding ground control. Whole-genome oligonucleotide microarray and high throughput proteomics which offer the possibility to survey respectively the global transcriptional and translational response of an organism were used to test the effect of space flight. Moreover in an effort to identify a specific stress response of R. rubrum to space flight ground simulation of space ionizing radiation and space gravity were performed under identical culture setup and growth conditions encountered during the actual space journey. This study is unique in combining the results from an actual space experiment with the corresponding space ionizing radiation and modeled microgravity ground simulations which lead to a more solid dissection of the different factors contribution acting in space flight conditions. Total RNA was extracted from R. rubrum S1H grown after 10 days in space flight or after 10 days in simulated ionizing radiation or simulated microgravity. Each microarray slide contained 3 technical repeats.

Tags: bioassay_data_transformation, feature_extraction, gravity, grow, hybridization, image_aquisition, labeling, nucleic_acid_extraction, p-gse14241-1, p-gse14241-10, p-gse14241-2, p-gse14241-3, p-gse14241-4, p-gse14241-6, p-gse14241-7, p-gse14241-8, p-gse14241-9, spaceflight
Organization: National Aeronautics and Space Administration
HARV replication of the BRIC-21 Bacillus subtilis spaceflight samples

Previous spaceflight experiments using Bacillus subtilis have reported altered transcriptome profiles during spaceflight compared to matching ground samples. This study tried to replicate those transcriptome changes using High Aspect Ratio Vessels (HARVs). B. subtilis spores were grown in HARVs using the same protocol and growth conditions as the BRIC-21 spaceflight mission. RNA was extracted from the HARV samples and sequenced for differential expression analysis. HARV differentially expressed genes were then compared to the genes identified as differentially expressed in the BRIC-21 mission to access the accuracy of HARVs as a model for spaceflight experiments.

Tags: library-construction, microgravity-simulation, nucleic-acid-extraction, nucleic-acid-sequencing, treatment-protocol
Organization: National Aeronautics and Space Administration
microRNA expression profiles in 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. microRNA expression profiling were carried out on total RNA extracted from PBLs of twelve healthy donors at the end of 24h-incubation time in MMG and in 1g conditions. Analyses were performed by using the Human miRNA Microarray kit (V2) (Agilent Technologies) that allows the detection of 723 known human (miRBase v.10.1) and 76 human viral miRNAs. By comparing the expression profile of MMG-incubated vs. 1g-incubated PBLs of the same donor we found 42 differentially expressed miRNAs 25 up-regulated and 17 down-regulated.

Tags: array-scanning-protocol, hybridization-protocol, individual, labelling-protocol, normalization-data-transformation-protocol, nucleic-acid-extraction-protocol, p-gse57400-1, p-gse57400-10, p-gse57400-11, p-gse57400-12, p-gse57400-13, p-gse57400-14, p-gse57400-15, p-gse57400-16, p-gse57400-17, p-gse57400-18, p-gse57400-19, p-gse57400-2, p-gse57400-20, p-gse57400-21, p-gse57400-22, p-gse57400-23, p-gse57400-24, p-gse57400-25, p-gse57400-26, p-gse57400-27, p-gse57400-28, p-gse57400-29, p-gse57400-3, p-gse57400-4, p-gse57400-5, p-gse57400-6, p-gse57400-7, p-gse57400-8, p-gse57400-9, sample-treatment-protocol, simulated-microgravity
Organization: National Aeronautics and Space Administration