AndreaBozzo/ceres-open-data-index huggingface dataset:
Transcriptome analysis of murine spleen in space

Our study aims to comprehensively understand effects induced by the space environment on mammals. To achieve this aim we analyze the male mice housed under environments as the artificial gravity and the microgravity (space environment) in Japanese Experiment Module JEM) of the International Space Station (ISS) on orbit for 35 days. After recovered these mice on the ground transcriptome analysis by next-generation sequencing technology is performed about spleen to examine alteration of gene expression in the space.

Tags: altered-gravity, animal-husbandry, data-transformation, genelab-rnaseq-data-processing-protocol, library-construction, mouse-habitation, nucleic-acid-extraction, nucleic-acid-sequencing, pre-launch-animal-acclimation, sample-collection, spaceflight
Organization: National Aeronautics and Space Administration
Synergistic effects of microgravity and space radiation (Nimblegen)

Space radiations and microgravity both could cause DNA damage in cells but the effects of microgravity on DNA damage response to space radiations are still controversial. A mRNA microarray and microRNA microarray in dauer larvae of Caenorhabditis elegans (C. elegans) that endured space xef xac x82ight environment and space radiations environment during 16.5-day Shenzhou-8 space mission were performed. In our study wild type dys-1 mutant and ced-1 mutant strains of C.elegans endured four conditions during shenzhou-8 spaceflight mission including spaceflight static condition(ss) spaceflight 1-g centrifugal condition(sc) ground control condition(gc) and no-transport control. Limited to the quantity of worm samples we performed technical-repeat test but not sample-repeat test.Accordingly 12 mRNA microarrays were performed.

Tags: absorbed-radiation-dose, data-collection, labeling, normalization-data-transformation, nucleic-acid-hybridization, rna-extraction, sample-collection, weightlessness
Organization: National Aeronautics and Space Administration
Dynamic gene expression response to altered gravity in human T cells (sounding rocket 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.

Tags: growth-protocol, labeling, microgravity, normalization-data-transformation, nucleic-acid-hybridization, rna-extraction, scan-protocol, treatment-protocol
Organization: National Aeronautics and Space Administration
Eruca sativa Rocket Science RNA-seq

In the   Rocket Science   citizen science project Eruca sativa (salad rocket) seeds stored for six months on board of the International Space Station caused delayed crop establishment. Here we investigated the physiological and molecular mechanisms underpinning the spaceflight effects on dry seeds. We found that   Space   seed germination vigor was reduced and aging sensitivity increased but the spaceflight did not compromise seed viability and the development of normal seedlings. Comparative analysis of the transcriptomes (using RNASeq) in dry seeds and upon controlled artificial aging treatment (CAAT) revealed differentially expressed genes (DEGs) associated with spaceflight and ageing. DEG categories enriched by spaceflight and CAAT included transcription and translation with reduced transcript abundances for 40S and 60S ribosomal subunit genes. Among the   spaceflight-up   DEGs were Heat Shock Protein (HSP) DNAJ-related chaperones a Heat Shock Factor (HSFA7a-like) and components of several DNA repair pathways (e.g. ATM DNA ligase1). The   response to radiation   category was especially enriched in   spaceflight-up   DEGs including HSPs catalases and the transcription factor HY5. The major finding from the physiological and transcriptome analysis is that spaceflight causes vigor loss and partial ageing during air-dry seed storage for which space environmental factors and consequences for seed storage during spaceflights are discussed.

Tags: library-construction, nucleic-acid-extraction, nucleic-acid-sequencing, sample-collection, spaceflight, treatment, treatment-protocol
Organization: National Aeronautics and Space Administration
miRNA signature detection and countermeasures against HZE radiation exposure for tissue degeneration-Heart tissue

Biological risks associated with space radiation and microgravity are major concerns for long-term space travel. Through a Systems Biology approach our previous NASA work has shown both TGF xce xb2 signaling pathways and miRNAs have a critical impact on defining health risks with and without space irradiation. We hypothesize that circulating microRNA (miRNA) signatures are driving microvascular disease and muscle degeneration associated with accelerating aging and will be enhanced by exposure to the space environment (radiation and microgravity). We investigated this hypothesis both in vivo and in vitro and test novel antagonist therapies to these miRNA signatures as countermeasures to reduce space radiation-induced health risks. A comprehensive Systems Biology approach was used to examine the influence by high atomic number by high (H) atomic number (Z) and energy (E) (HZE) irradiation. To simulate low-dose exposure due to galactic cosmic rays (GCR) we used the ions energy and doses determined by a NASA consensus formula of 7 different ions to represent GCR (referred to as GCR sim model). To simulate high-dose radiation exposure due to solar particle events (SPE) we used an acute dose of SPE simulated beam at 1Gy which has energies ranging from 50MeV to 150MeV. C57BL/6 wild-type mice were utilized for irradiation with our established simulated microgravity model (hindlimb suspension model) and an in vitro 3D microvasculature tissue model under simulated microgravity (clinostat) conditions will also be irradiated. To expand on the circulating miRNA signature determined from our preliminary data we determined a group of conserved miRNAs which are commonly being regulated in the majority of the organs and tissues throughout the host using our established techniques. MiRNA-sequencing on serum (before IR and at time of sacrifice) liver heart and muscle tissue for all radiation groups revealed the key circulating miRNA signature (consisting of multiple miRNAs) impacting disease risk. Collectively understanding of how whole body space radiation impacts microvascular and tissue degeneration through circulating miRNAs will greatly enhance health risk prognostication and provide possible new mechanisms for protection against space radiation.

Tags: hindlimb-unloading, ionizing-radiation, library-construction, nucleic-acid-extraction, nucleic-acid-sequencing, treatment-protocol
Organization: National Aeronautics and Space Administration
Low dose (0.04 Gy) irradiation (LDR) and hindlimb unloading (HLU) microgravity in mice: retina transcriptomic and epigenomic data

The purpose of the present study was to evaluate damage in brain and eye in a ground-based model for spaceflight which includes prolonged unloading and low-dose radiation. Low-dose/Low-dose-rate (LDR) gamma-radiation using 57Co plates (0.04 Gy) was delivered whole-body to mature 6-month old female C57BL/6 mice to simulate the radiation component. Anti-orthostatic tail suspension was used to model the unloading fluid shift and physiological stress aspects of the microgravity component. Mice were hindlimb suspended and/or irradiated for 21 days. Tissues were collected at 7 days 1 and 4 months following simulated microgravity. Herein we proposed to use omics-based molecular phenotyping approach for identification and characterization of genomic signatures in multiple organ system associated with low-dose radiation and simulated microgravity.

Tags: data-transformation, dna-sequencing-library-construction, genelab-rnaseq-data-processing-protocol, hindlimb-unloading, ionizing-radiation, nucleic-acid-extraction, nucleic-acid-sequencing, rna-sequencing-library-construction, sample-collection, spike-in-protocol, time-of-sample-collection-after-treatment, treatment-protocol
Organization: National Aeronautics and Space Administration
Jason-1 GDR version E NetCDF Geodetic

The Jason-1 Geophysical Data Records (GDR) Geodetic Mission contain full accuracy altimeter data, with a high precision orbit, provided approximately 35 days after data collection. The data are sorted into cycles that are approximately 11 days long and contain 280 pass files.  The instruments on Jason-1 make direct observations of the following quantities: altimeter range, significant wave height, ocean radar backscatter cross-section (a measure of wind speed), ionospheric electron content (derived by a simple formula), tropospheric water content, mean sea surface, and position relative to the GPS satellite constellation. The GDR contain all relevant corrections needed to calculate the sea surface height.

Tags: earth-science, ocean-waves, oceans, sea-surface-topography
Organization: National Aeronautics and Space Administration
Transcriptomic analysis of liver from mice subjected to simulated spaceflight euthanasia freezing and tissue preservation protocols

To understand the molecular mechanisms affected by spaceflight it is essential to achieve high quality sample preservation on-orbit for downstream gene expression analysis. However sample preservation protocols must also be compatible with available equipment and crew time. NASA  s Rodent Research (RR) missions have used various methods for euthanasia carcass preservation and tissue preservation. This study extends the sample preservation study performed by GeneLab in GLDS-49 which examined conditions used for the RR-1 mission to include conditions used for multiple RR missions and is designed to help determine factors which may confound data analysis. To determine whether these various factors affect changes in gene expression this ground-based study generated gene expression profiles measured by RNAseq from the livers of 20-21 week-old female C57BL/6J mice. Multiple interacting factors were investigated: 1) To understand how euthanasia protocols affect gene expression when mouse carcasses are slow frozen mice were euthanized by either euthasol injection ketamine/xylazine injection or CO2 inhalation and carcasses slow frozen on dry-ice mimicking carcass preservation in the MELFI on the ISS. Carcasses were thawed and RNA extracted from livers; 2) To understand how carcass preservation protocols affect gene expression mice were euthanized with euthasol and carcasses preserved by flash freezing in liquid nitrogen slow freezing on dry ice or immersion in RNAlater following three-way segmentation. Carcasses were thawed and RNA extracted from livers; 3) To understand how tissue preservation protocols affect gene expression mice were euthanized with euthasol and livers dissected and processed immediately or preserved by flash freezing in liquid nitrogen slow freezing on dry ice or immersion in RNAlater. Liver samples that were processed immediately were homogenized in RLT buffer and then either immediately further processed for RNA extraction or were stored for 70 days at -80C post-homogenization in sample RLT buffer prior to RNA extraction.

Tags: carcass-preservation-method, data-transformation, dissection-condition, euthanasia, euthanasia-animal, euthanasia-method, genelab-rnaseq-data-processing-protocol, library-construction, nucleic-acid-extraction, nucleic-acid-sequencing, sample-collection, spike-in-control, spike-in-control-protocol, tissue-homogenate-preservation-time-at-80c-in-rlt-buffer, tissue-preservation-method
Organization: National Aeronautics and Space Administration
Biological Research in Canisters-16 (BRIC-16): Investigations of the plant cytoskeleton in microgravity with gene profiling and cytochemistry

These investigations studied the fundamentals of how plants perceive gravity and develop in microgravity. It informs how gene regulation is altered by spaceflight conditions.

Tags: cosmic-radiation, data-collection, data-processing, data-transformation, genelab-microarray-data-processing-protocol, growth-protocol, labeling, nucleic-acid-hybridization, radiation-dosimetry, rna-extraction, sample-collection, spaceflight
Organization: National Aeronautics and Space Administration
Transcriptomic analysis of spleens 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 spleens 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 spleens collected 7 days following treatment. RNA sequencing data was generated to assess transcriptional changes in these spleens.

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
Low dose ionizing radiation treated lymphoblastoid cells

Irradiated cell lines exposed to 1-10 cGy 2 Lymphoblastoid cell lines (GM15510 and GM15036) irradiated 1 2.5 5 7.5 10 cGy RNA is isolated and labeled using a T7 amplification Arcturus kit for hybridization on triplicate arrays.

Tags: absorbed-radiation-dose, bioassay_data_transformation, cell-line, data-transformation, feature_extraction, genelab-microarray-data-processing-protocol, grow, hybridization, image_aquisition, ionizing-radiation, labeling, nucleic_acid_extraction, p-gse22639-1, p-gse22639-2, p-gse22639-3, p-gse22639-4, p-gse22639-5, p-gse22639-6, p-gse22639-7, p-gse22639-8, specified_biomaterial_action
Organization: National Aeronautics and Space Administration
Spaceflight effects on the mouse retina: Histological gene expression and epigenetic changes after flight on STS-135

We report the findings of an animal experiment onboard STS-135 investigating the molecular aspects of the impact of spaceflight on retinal biology by performing differential gene expression profiling between mice flown onboard STS-135 and their ground control counterparts.

Tags: cosmic-radiation, data-transformation, genelab-microarray-data-processing-protocol, growth-protocol, labeling, normalization-data-transformation, nucleic-acid-hybridization, radiation-dosimetry, rna-extraction, sample-collection, spaceflight
Organization: National Aeronautics and Space Administration
Expression data from rice calli cultured with 2,4-D

Four days old rice calli were selected to grow 324h under spaceflight controls 1g-flight controls and 1g-ground controls. We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process. Rice calli were selected at different treatment for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain the diff-genes that caused by the microgravity.

Tags: altered-gravity, data-collection, growth-protocol, labeling, nucleic-acid-hybridization, rna-extraction, sample-collection, spaceflight, treatment-protocol
Organization: National Aeronautics and Space Administration
A study of alterations DNA epigenetic modifiincations (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 2 different DNA modifications with 2 replicates each for 1 cell type.

Tags: growth, growth-protocol, library-construction, microgravity-simulation, nucleic-acid-extraction, nucleic-acid-sequencing, treatment, treatment-protocol
Organization: National Aeronautics and Space Administration
Rodent Research-1 (RR1) NASA Validation Flight: Mouse liver transcriptomic proteomic and epigenomic data

RR-1 is a validation flight to evaluate the hardware operational and science capabilities of the Rodent Research Project on the ISS. RNA DNA and protein were purified from liver tissues from RR-1 mice (female C57BL/6J 16wk old at time of launch). From each group two liver samples were collected and frozen immediately after euthanasia. The rest of the liver samples from each group were collected from frozen carcasses dissected post-flight. RNA-Seq whole genome and RNA BS-Seq (bisulfite sequencing) and proteomic expression profiling were performed. RNA extracted from these tissues was re-sequenced; these data are available as part of GLDS-168 (https://genelab-data.ndc.nasa.gov/genelab/accession/GLDS-168).

Tags: 5mc-total-rna-methylation-analysis, animal-and-tissue-sampling, animal-husbandry, data-transformation, dissection-condition, dna-library-construction, epitranscriptomics, extraction, genelab-rnaseq-data-processing-protocol, histology, labeling, library-construction, mass-spectrometry, mass-spectrometry-protocol, mouse-habitation, nucleic-acid-extraction, nucleic-acid-sequencing, protein-extraction, proteomics-data-transformation, rna-sequencing-library-construction, sample-collection, spaceflight, tmt-isobaric-labeling
Organization: National Aeronautics and Space Administration
NCHS - Potentially Excess Deaths from the Five Leading Causes of Death

MMWR Surveillance Summary 66 (No. SS-1):1-8 found that nonmetropolitan areas have significant numbers of potentially excess deaths from the five leading causes of death. These figures accompany this report by presenting information on potentially excess deaths in nonmetropolitan and metropolitan areas at the state level. They also add additional years of data and options for selecting different age ranges and benchmarks.

Potentially excess deaths are defined in MMWR Surveillance Summary 66(No. SS-1):1-8 as deaths that exceed the numbers that would be expected if the death rates of states with the lowest rates (benchmarks) occurred across all states. They are calculated by subtracting expected deaths for specific benchmarks from observed deaths.

Not all potentially excess deaths can be prevented; some areas might have characteristics that predispose them to higher rates of death. However, many potentially excess deaths might represent deaths that could be prevented through improved public health programs that support healthier behaviors and neighborhoods or better access to health care services.

Mortality data for U.S. residents come from the National Vital Statistics System. Estimates based on fewer than 10 observed deaths are not shown and shaded yellow on the map.

Underlying cause of death is based on the International Classification of Diseases, 10th Revision (ICD-10)

Heart disease (I00-I09, I11, I13, and I20–I51)
Cancer (C00–C97)
Unintentional injury (V01–X59 and Y85–Y86)
Chronic lower respiratory disease (J40–J47)
Stroke (I60–I69)
Locality (nonmetropolitan vs. metropolitan) is based on the Office of Management and Budget’s 2013 county-based classification scheme.

Benchmarks are based on the three states with the lowest age and cause-specific mortality rates.

Potentially excess deaths for each state are calculated by subtracting deaths at the benchmark rates (expected deaths) from observed deaths.

Users can explore three benchmarks:

“2010 Fixed” is a fixed benchmark based on the best performing States in 2010.
“2005 Fixed” is a fixed benchmark based on the best performing States in 2005.
“Floating” is based on the best performing States in each year so change from year to year.
 
SOURCES

CDC/NCHS, National Vital Statistics System, mortality data (see http://www.cdc.gov/nchs/deaths.htm); and CDC WONDER (see http://wonder.cdc.gov).

REFERENCES 

1. Moy E, Garcia MC, Bastian B, Rossen LM, Ingram DD, Faul M, Massetti GM, Thomas CC, Hong Y, Yoon PW, Iademarco MF. Leading Causes of Death in Nonmetropolitan and Metropolitan Areas – United States, 1999-2014. MMWR Surveillance Summary 2017; 66(No. SS-1):1-8.

2. Garcia MC, Faul M, Massetti G, Thomas CC, Hong Y, Bauer UE, Iademarco MF. Reducing Potentially Excess Deaths from the Five Leading Causes of Death in the Rural United States. MMWR Surveillance Summary 2017; 66(No. SS-2):1–7.

Tags: cancer, chronic-lower-respiratory-disease, heart-disease, stroke, unintentional-injury
Organization: U.S. Department of Health & Human Services
Provisional COVID-19 Deaths by Week and County Social Vulnerability Index

Effective September 27, 2023, this dataset will no longer be updated. Similar data are accessible from wonder.cdc.gov.

Deaths involving COVID-19 reported to NCHS by week and county Social Vulnerability Index (SVI) in the United States. SVI scores are from CDC/ASTDR's Geospatial Research, Analysis & Service Program 2018 database. These scores range from 0 to 1, and categorized as low (0-0.333), moderate (0.334-0.666) or high (0.667-1).

More information on SVI can be found here: https://www.atsdr.cdc.gov/placeandhealth/svi/index.html

Tags: all-causes, coronavirus, covid-19, deaths, mortality, nchs, nvss, provisional, social-vulnerability-index, united-states, weekly
Organization: U.S. Department of Health & Human Services
Monthly Provisional Counts of Deaths by Select Causes, 2020-2023

Effective September 27, 2023, this dataset will no longer be updated. Similar data are accessible from wonder.cdc.gov.

Provisional counts of deaths by the month the death occurred and by select causes of death for 2020-2023.

Tags: all-causes, alzheimer-disease, cancer, causes-of-death, cerebrovascular-disease, chronic-lower-respiratory-disease, coronavirus, covid-19, deaths, diabetes, diseases-of-heart, drug-overdose, homicide, influenza, kidney-disease, monthly, mortality, motor-vehicle-accidents, natural-cause, nchs, nvss, pneumonia, provisional, respiratory-disease, septicemia, suicide, unintentional-injuries, united-states
Organization: U.S. Department of Health & Human Services
Weekly Counts of Deaths by Jurisdiction and Age

Effective September 27, 2023, this dataset will no longer be updated. Similar data are accessible from wonder.cdc.gov.

This visualization provides weekly data on the number of deaths from all causes by jurisdiction of occurrence and age group. Counts of deaths in more recent weeks can be compared with counts from earlier years to determine if the number is higher than expected.

Tags: age, age-group, all-causes, deaths, mortality, nchs, nvss, provisional, puerto-rico, state, united-states, weekly
Organization: U.S. Department of Health & Human Services