AndreaBozzo/ceres-open-data-index huggingface dataset:
RNA sequencing of zebrafish embryos under simulated microgravity conditions

To reveal the potential mechanisms involved in the dysfunction of antiviral immune responses under simulated microgravity conditions, we investigated the transcriptional changes related to the status of innate immune responses by RNA-seq with poly I:C or mock PBS treatment under Normal gravity or simulated microgravity conditions. Our results indicate that the retinoic acid inducible gene (RIG)-I-like receptor (RLR) and Toll-like receptor (TLR) signal pathways, which are both involved in the type-I interferon induction, are significantly inhibited by simulated microgravity effects.

Tags: microgravity-simulation-treatment, treatment-protocol-nucleic-acid-extraction-library-construction-nucleic-acid-sequencing
Organization: National Aeronautics and Space Administration
Effect of microgravity on HUVECs (Human Umbilical vein Endothelial cells) cells and its transcriptome analysis.

Adaptation of humans in low gravity conditions is a matter of utmost importance when efforts are on to a gigantic leap in human space expeditions for tourism and formation of space colonies. In this connection cardiovascular adaptation in low gravity is a critical component of human space exploration. Deep high-throughput sequencing approach allowed us to analyze the miRNA and mRNA expression profiles in human umbilical cord vein endothelial cells (HUVEC) cultured under gravity (G) and stimulated microgravity (MG) achieved with a clinostat. The present study identified totally 1870 miRNAs differentially expressed in HUVEC under MG condition when compared to the cells subjected to unitary G conditions. The functional association of identified miRNAs targeting specific mRNAs revealed that miRNAs hsa-mir-496 hsa-mir-151a hsa-miR-296-3p hsa-mir-148a hsa-miR-365b-5p hsa-miR-3687 hsa-mir-454 hsa-miR-155-5p and hsa-miR-145-5p differentially regulated the genes involved in cell adhesion angiogenesis cell cycle JAK-STAT signaling MAPK signaling nitric oxide signaling VEGF signaling and wound healing pathways. Further the q-PCR based experimental studies of upregulated and downregulated miRNA and mRNAs demonstrate that the above reported miRNAs influence the cell proliferation and vascular functions of the HUVEC in MG conditions effectively. Consensus on the interactome results indicates restricted fluctuations in the transcriptome of the HUVEC exposed to short-term MG that could lead to higher levels of endothelial functions like angiogenesis and vascular patterning.

Tags: growth-protocol, library-construction, microgravity-simulation, nucleic-acid-extraction, nucleic-acid-sequencing, treatment-protocol
Organization: National Aeronautics and Space Administration
Effect of microgravity on brain gene expression in mice

Changes in gravitational force such as that experienced by astronauts during space flight induce a redistribution of fluids from the caudad to the cephalad portion of the body together with an elimination of normal head-to-foot hydrostatic pressure gradients. To assess brain gene profile changes associated with microgravity and fluid shift a large-scale analysis of mRNA expression levels was performed in the brains of 2 weeks control and hindlimb-unloaded (HU) mice using cDNA microarrays. Although to different extent all functional categories displayed significantly regulated genes indicating that considerable transcriptomic alterations are induced by HU. Interestingly the TIC class (transport of small molecules and ions into the cells) had the highest percentage of up-regulated genes while the most down-regulated genes were those of the JAE class (Cell junction Adhesion Extracellular Matrix). TIC genes comprised 16% of those whose expression was altered including sodium channel nonvoltage-gated 1 beta (Scnn1b) glutamate receptor (Grin1) voltage-dependent anion channel 1 (Vdac1) calcium channel beta 3 subunit (Cacnb3) and others. The analysis performed by GeneMAPP revealed several altered protein classes and functional pathways such as blood coagulation and immune response learning and memory ion channels and cell junction. In particular data indicate that HU causes an alteration in hemostasis which resolves in a shift toward a more hyper-coagulative state with an increased risk of venous thrombosis. Furthermore HU treatment seems to impact on key steps of synaptic plasticity and learning processes. We used brains of four control (C1 C2 C3 C4) and four tail-suspended hindlimb-unloaded (E1 E2 E3 E4) mice to ensure statistical relevance of the study. 60 ug of total RNA extracted in TRIzol from each brain was reversed transcribed into labeled cDNAs using fluorescent Cy5 or Cy3-dUTP (Amersham Biosciences NJ). Differently labeled cDNAs obtained from a pair of biological replicas were co-hybridized overnight at 50C with a microscope slide spotted with ~ 27,000 mouse cDNA sequences produced by the Microarray Core Facility of the Albert Einstein College of Medicine in the  xef xbf xbdmultiple yellow xef xbf xbd design (i.e.: C1C2 C3C4 E1E2 E3E4) described in Iacobas DA Fan C Iacobas S et al. Transcriptomic changes in developing kidney exposed to chronic hypoxia. Biochem Biophys Res Commun. 2006 349(1):329-38).

Tags: bioassay_data_transformation, feature_extraction, grow, hindlimb-unloading, hybridization, image_aquisition, labeling, nucleic_acid_extraction, p-gse12312-1, p-gse12312-10, p-gse12312-11, p-gse12312-2, p-gse12312-3, p-gse12312-4, p-gse12312-5, p-gse12312-6, p-gse12312-7, p-gse12312-8, p-gse12312-9, specified_biomaterial_action
Organization: National Aeronautics and Space Administration
MicroRNA expression of C. elegans in space environment

Entire microRNA expression were analyzed using the Filgen Array miRNA Caenorhabditis elegans 232 probes (Filgen). In the microRNA expression analysis we compared the expression data between two groups: micro-gravity samples (4 d and 8 d) and controls (4 d and 8 d ground control and 1 G centrifuge onboard ISS).

Tags: data-processing, gravity, growth-protocol, labeling, nucleic-acid-hybridization, rna-extraction, sample-treatment-protocol, scan-protocol, timepoint
Organization: National Aeronautics and Space Administration
Multi-omic investigations of mouse liver subjected to simulated spaceflight freezing and storage protocols

This study compares standard laboratory protocols for tissue freezing and storage with a simulation of the delayed processing of liver specimens and long-term storage protocols used during the Rodent Research-1 (RR-1) payload. Liver samples from twelve-week old female C57/BL6 mice (snap frozen vs. 25 min. slow-frozen and stored for 3 days vs. 1 year) received from the RR-1 project were processed for extraction of RNA DNA and protein. RNA-seq whole genome bisulfite sequencing and mass spectrometry proteomics were performed. These multi-omics datasets will help distinguish the effects of freezing and storage time that could confound the interpretation of the Rodent Research-1 datasets.

Tags: animal-and-tissue-sampling, extraction, freezing-profile, labeling, library-construction, mass-spectrometry, nucleic-acid-extraction, nucleic-acid-sequencing, protein-extraction, proteomic-labeling, sample-collection, tissue-storage-time
Organization: National Aeronautics and Space Administration
Expression profiling of soleus muscle under the effect of simulated spaceflight

Spaceflight imposes the risk of skeletal muscle atrophy for astronauts. The understanding of muscle atrophy because of spaceflight is limited but continued efforts are essential for developing countermeasures of this effect. A distinct difference between spaceflight-induced muscle atrophy and other forms of atrophy is the additional effect of cosmic rays in outer space. To study spaceflight-induced muscle atrophy we performed two ground-based models of microgravity in a low dose radiation environment and studied transcriptional changes in rat soleus muscle using microarray technology.

Tags: clinical-treatment, data-transformation, growth-protocol, hindlimb-unloading, labeling, nucleic-acid-hybridization, rna-extraction
Organization: National Aeronautics and Space Administration
Environmental and facility conditions promote singular gravity responses of transcriptome during Drosophila metamorphosis

Genome-wide transcriptional profiling showed that reducing gravity levels in the International Space Station (ISS) causes important alterations in Drosophila gene expression intimately linked to imposed spaceflight-related environmental constrains during Drosophila metamorphosis. However simulation experiments on ground testing space-related environmental constraints show differential responses. Curiously although particular genes are not common in the different experiments the same GO groups including a large multigene family related with behavior stress response and organogenesis are over represented in them. A global and integrative analysis using the gene expression dynamics inspector (GEDI) self-organizing maps reveals different degrees in the responses of the transcriptome when using different environmental conditions or microgravity/hypergravity simulation devices. These results suggest that the transcriptome is finely tuned to normal gravity. In regular environmental conditions the alteration of this constant parameter on Earth can have mild effects on gene expression but when environmental conditions are far from optimal the gene expression is much more intense and consistent effects.

Tags: altered-gravity, altered-gravity-simulator, data-transformation, genelab-microarray-data-processing-protocol, growth-protocol, labeling, nucleic-acid-hybridization, o2-level, rna-extraction, scan-protocol, temperature, treatment-protocol
Organization: National Aeronautics and Space Administration
Turbulent boundary layer wall pressure flight data

Wall pressure data acquired during flight tests at three flight conditions are provided: 48k feet altitude at Mach 0.86; 32k feet at Mach 0.70; and 24k feet at Mach 0.56. Details of the flight test, sensors, and sensor locations are given in a journal article that is referenced in the supporting documents datafile.

Tags: turbulent-boundary-layer
Organization: National Aeronautics and Space Administration
Alteration of Proteomes in First-generation Cultures of Bacillus pumilus Spores Exposed to Outer Space

Bacillus pumilus SAFR-032 was originally isolated from the Jet Propulsion Lab Spacecraft Assembly Facility and thoroughly characterized for its enhanced resistance to UV irradiation and oxidative stress. This unusual resistance of SAFR-032 is of particular concern in the context of planetary protection and calls for development of novel disinfection techniques to prevent extraterrestrial contamination. Previously spores of SAFR-032 were exposed for 18 xe2 x80 x89months to a variety of space conditions on board the International Space Station to investigate their resistance to Mars-like conditions and space travel. Here proteomic characterization of vegetative SAFR-032 cells from space-surviving spores is presented in comparison to a ground control. Vegetative cells of the first passage were processed and subjected to quantitative proteomics using tandem mass tags. Approximately 60% of all proteins encoded by SAFR-032 were identified and 301 proteins were differentially expressed among the strains. We found that proteins predicted to be involved in carbohydrate transport/metabolism and energy production/conversion had lower abundance than those of the ground control. For three proteins we showed that the expected metabolic activities were decreased as expected with direct enzymatic assays. This was consistent with a decrease of ATP production in the space-surviving strains. The same space-surviving strains showed increased abundance of proteins related to survival growth advantage and stress response. Such alterations in the proteomes provide insights into possible molecular mechanisms of B. pumilus SAFR-032 to adapt to and resist extreme extraterrestrial environments.

Tags: data-transformation, growth-protocol, labeling, mass-spectrometry, protein-extraction, spaceflight, treatment
Organization: National Aeronautics and Space Administration
Effects of bedrest and hypoxia on human skeletal muscle miRNA expression

The present study concerns the effects of 21 days of sustained recumbence (bedrest) and hypoxia alone and in combination on skeletal muscle microRNA expression. 14 male subjects participated in 3 experimental campaigns in a counterbalanced fashion: normoxic bedrest (NBR) hypoxic bedrest (HBR) and hypoxic ambulatory confinement (HAMB) both hypoxic conditions with FO2 = 0.141 and PIO2 = 90  xc2 xb1 0.4 mmHg equivalent to an altitude of  xe2 x89 x88 4000 m). Each intervention (bedrest or ambulatory confinement) lasted 21 days and the interventions were separated by a 4-month wash-out/recovery period. The order in which each subject undertook the interventions is denoted   Intervention_order   Throughout both bedrest interventions each subject remained in a horizontal position at all times. He was allowed one pillow for the head and to occasionally lean on an elbow while eating or being transferred to a gurney. Muscular exercise was prohibited. During the HAMB confinement each subject was allowed to move freely within the hypoxic area. To mimic a normal level of physical activity subjects performed 30 minutes of low-to-moderate-intensity exercise twice daily. Muscle samples from Vastus lateralis.

Tags: bed-rest, experimental-campaign, labeling, normalization-data-transformation, nucleic-acid-hybridization-and-data-collection, rna-extraction, sample-collection, sample-collection-protocol, sampling-time, scan-protocol, treatment, treatment-protocol
Organization: National Aeronautics and Space Administration
A study of gene expression 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: data-processing, data-transformation, genelab-rnaseq-data-processing-protocol, growth-protocol, library-construction, microgravity-simulation, nucleic-acid-extraction, nucleic-acid-sequencing, treatment-protocol
Organization: National Aeronautics and Space Administration
MODIS Cloud Regimes and Cloud-Precipitation Hybrid Regimes (MODIS-IMERG)

Cloud regimes and Cloud-Precipitation Hybrid Regimes are derived via k-means clustering, with MODIS C6.1 2D joint histogram of CTP and COT (total 42 bins) and IMERG v06B precipitation histogram (total 6 bins) in 50S-50N and 15S-15N domain.

By the relative weight between cloud and precipitation, there are 4 kinds of regime sets for each tropical and extended domain:
1) Cloud only (42 bins), 
2) Cloud+Precipitation with weight 1 (Cld42+Pr6x1; 48 bins), 
3) Cloud+Precipitation with weight 3 (Cld42+Pr6x3; 60 bins), 
4) Cloud+Precipitation with weight 7 (Cld42+Pr6x7; 84 bins; equal weight).

Reference
Jin et al. (2020; JAMC, submitted)

Tags: cloud, cloud-precipitation-hybrid-regime, cloud-regime, imerg, modis, precipitation
Organization: National Aeronautics and Space Administration
Environmental and facility conditions promote singular gravity responses of transcriptome during Drosophila metamorphosis

Genome-wide transcriptional profiling showed that reducing gravity levels in the International Space Station (ISS) causes important alterations in Drosophila gene expression intimately linked to imposed spaceflight-related environmental constrains during Drosophila metamorphosis. However simulation experiments on ground testing space-related environmental constraints show differential responses. Curiously although particular genes are not common in the different experiments the same GO groups including a large multigene family related with behavior stress response and organogenesis are over represented in them. A global and integrative analysis using the gene expression dynamics inspector (GEDI) self-organizing maps reveals different degrees in the responses of the transcriptome when using different environmental conditions or microgravity/hypergravity simulation devices. These results suggest that the transcriptome is finely tuned to normal gravity. In regular environmental conditions the alteration of this constant parameter on Earth can have mild effects on gene expression but when environmental conditions are far from optimal the gene expression is much more intense and consistent effects.

Tags: growth-protocol, labeling, magnetic-field, normalization-data-transformation, nucleic-acid-hybridization, o2, rna-extraction, scan-protocol, stimulated-gravity-g-level, temperature, treatment-protocol
Organization: National Aeronautics and Space Administration
Zebrafish larvae submitted to simulated microgravity on a clinostat (CLINO) at 5dpf for one day

The general objective of the study was to determine modulation of gene expression by environmental factors specifically simulation of microgravity with a special emphasis on bone formation. For this reason the specific period of treatment was chosen between 5-6 days post-fertilization (dpf) when bone formation and calcification are taking place. Zebrafish larvae were placed at 5 dpf into a clinostat (CLINO) for 24 hours which was shown to simulate microgravity by the specific rotational movements it generates. We show that CLINO exposure causes a clear decrease of bone formation as illustrated by cranial skeleton staining of the bone matrix by Alizarin Red by morphometric analysis of the resulting images. Thus a whole genome micro-array experiment was conducted to identify genes that may be involved in the observed effect on bone formation.

Tags: array-scanning-and-feature-extraction, growth-protocol, labeling, normalization-data-transformation, nucleic-acid-hybridization, p-mtab-48667, p-mtab-48668, p-mtab-48669, p-mtab-48670, p-mtab-48671, p-mtab-48672, p-mtab-48673, rna-extraction, stress, treatment-protocol
Organization: National Aeronautics and Space Administration
OMPS-N20 NM PCA SO2 Step 1 Total Column 1-Orbit L2 Swath 17x13km

The OMPS-N20_NM_PCA_SO2 Step1 Total Column 1-Orbit L2 Swath 17x13km collection 1 product contains the retrieved sulfur dioxide (SO2) measured by the Ozone Mapping and Profiling Suite (OMPS) Nadir-Mapper (NM) sensor on the NOAA-20 (JPSS-1) satellite. The product is based on the NASA Goddard Space Flight Center principal component analysis (PCA) spectral fitting algorithm (Li et al., 2013, 2017) used to retrieve the SO2 total column amounts assuming different SO2 plume heights, including the boundary layer (lowest 1 km of the atmosphere), the lower (centered at 3 km), middle (centered at 8 km) and upper (centered at 13 km) troposphere, as well as the lower stratosphere (centered at 18 km).

Each granule contains data from the daylight portion for a single orbit or about 50 minutes. Spatial coverage is global (-90 to 90 degrees latitude), and there are about 14 orbits per day each with a swath width of 2600 km. There are 104 pixels in the cross-track direction before February 13, 2019 with a pixel resolution of about 17 km x 17 km at nadir. Since then, the pixel resolution has been enhanced to 17 km x 13 km at nadir, with 140 pixels in the cross-track direction. The files are written using netCDF version 4.

Tags: atmosphere, atmospheric-chemistry, earth-science
Organization: National Aeronautics and Space Administration
Dynamic gene expression response to altered gravity in human T cells (parabolic flight)

We investigated differentially regulated genes in human Jurkat T lymphocytic cells in 20s and 5min microgravity and in hypergravity and compared expression profiles to identify potential gravity-regulated genes and adaptation processes. This dataset is part of a series of three and the other two datasets are deposited in GLDS-188 and GLDS-189.

Tags: growth-protocol, hypergravity, labeling, microgravity, normalization-data-transformation, nucleic-acid-hybridization, nucleic-acid-hybridization-to-array-protocol, rna-extraction, scan-protocol, treatment-protocol
Organization: National Aeronautics and Space Administration
Salivary microbiome sequencing of astronauts

This study  s goal was to examine if any salivary microbiome changes were observed in astronauts as a result of spaceflight. In addition this study looked for any microbiome signature that may be associated with viral reactivation in humans

Tags: data-transformation, genelab-amplicon-seq-data-processing-protocol, library-construction, nucleic-acid-extraction, nucleic-acid-sequencing, sample-collection, spaceflight, time
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

Efficient generation of cardiomyocytes from human pluripotent stem cells is critical for their regenerative applications. Microgravity and 3D culture can profoundly modulate cell proliferation and survival. Here we engineered microscale progenitor cardiac spheres from human pluripotent stem cells and exposed the spheres to simulated microgravity using a random positioning machine for 3 days during their differentiation to cardiomyocytes. 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: data-transformation, genelab-rnaseq-data-processing-protocol, library-construction, microgravity-simulation, normalization-data-transformation-protocol, nucleic-acid-extraction, nucleic-acid-sequencing, p-gse84582-1, p-gse84582-2, treatment-protocol
Organization: National Aeronautics and Space Administration