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8,071 results for “transcriptome analysis”
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.
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.
RNA-Seq transcriptome analysis of reactive oxygen species gene network in Mizuna plants grown in long-term space flight
Space environment is suspected to generate reactive oxygen species (ROS) and induce oxidative stress in plants however little is known about the gene expression of ROS gene network in plants grown in long-term space flight. RNA-Seq was used to define the large-scale gene expression profiles of Mizuna harvested after 27 days cultivation in the international space station to understand the molecular response and adaptation to space environment.Results: Total reads of transcripts from the Mizuna grown in the international space station as well as on the ground by RNA-Seq using next generation sequencing technology showed 8,258 and 14,170 transcripts up- and down-regulated in the space-grown Mizuna respectively when compared with those from the ground-grown Mizuna. A total of 20 in 32 ROS oxidative marker genes were up-regulated including high expression of 4 hallmarks and preferentially expressed gene associated with ROS-scavenging genes was thioredoxin glutaredoxin and alternative oxidase genes. In the transcription factors of ROS gene network MEKK1-MKK4-MPK3 OXI1-MKK4-MPK3 and OXI1-MPK3 of MAP cascades induction of WRKY22 by MEKK1-MKK4-MPK3 cascade induction of WRKY25 and repression of ZAT7 by Zat12 were suggested. RbohD and RbohF genes were up-regulated preferentially in NADPH oxidase genes which produce ROS.Conclusions: Our large-scale transcriptome analysis demonstrated that the space environment induced oxidative stress and ROS gene network was activated in the space-grown Mizuna some of which were common genes up-regulated by abiotic and biotic stress and were preferentially up-regulated genes by the space environment even though Mizuna grew in the space as well as on the ground showing that plants could acclimate to the space environment by reprograming the expression of ROS gene network.
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.
Transcriptomic analysis of quadriceps 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 quadriceps 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 quadriceps; 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 quadriceps; 3) To understand how tissue preservation protocols affect gene expression mice were euthanized with euthasol and quadriceps immediately dissected and preserved by flash freezing in liquid nitrogen slow freezing on dry ice or immersion in RNAlater.
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.
Transcriptome analysis of germinating maize kernels exposed to smoke-water and the active compound KAR1
GEO Series GSE17484. Zea mays. 68 samples. Type: Expression profiling by array.
Transcriptome profiling and digital gene expression analysis of sweet potato challenged with Fusarium oxysporum f. sp.batatas.
GEO Series GSE89290. Ipomoea batatas. 16 samples. Type: Expression profiling by high throughput sequencing.
Transcriptomic and phenotypic analysis reveals new functions for the Tat pathway in Yersinia pseudotuberculosis
GEO Series GSE80532. Yersinia pseudotuberculosis IP 32953; Yersinia pseudotuberculosis. 16 samples. Type: Expression profiling by array.
Transcriptome analysis of human periodontal ligament cells under tensile loading
GEO Series GSE173891. Homo sapiens. 10 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
Whole transcriptome analysis of brain hippocampal tissue from SAMP8 mice and rat primary neurons treated with the Alzheimer’s disease drug candidate CAD031
GEO Series GSE108776. Mus musculus; Rattus norvegicus. 9 samples. Type: Expression profiling by high throughput sequencing.
Transcriptome analysis of wild type and RAR deficient frog faces during development
GEO Series GSE116819. Xenopus laevis. 6 samples. Type: Expression profiling by high throughput sequencing.
Integrative genomic, transcriptomic and RNAi analysis indicates a potential oncogenic role for FAM110B in castration-resistant prostate cancer.
GEO Series GSE28403. Homo sapiens. 47 samples. Type: Expression profiling by array; Genome variation profiling by genome tiling array.
Transcriptome analysis of circulating monocytes in obese patients before and three months after bariatric surgery
GEO Series GSE32575. Homo sapiens. 48 samples. Type: Expression profiling by array.
Transcriptome analysis of post-hatch breast muscle in legacy and modern broiler chickens reveals enrichment of several regulators of myogenic growth
GEO Series GSE65217. Gallus gallus. 23 samples. Type: Expression profiling by high throughput sequencing.
Transcriptomic analysis uncovers an unfolded protein response in ADNP syndrome
GEO Series GSE280293. Homo sapiens. 27 samples. Type: Expression profiling by high throughput sequencing.
Transcriptomic analysis of neuroblastoma cells in response to stable over-expression of Ets-1 promoter-associated noncoding RNA (pancEts-1)
GEO Series GSE104950. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
Next generation sequencing transcriptome analysis of colonic epithelial cells from bone marrow transplant recipient mice
GEO Series GSE158259. Mus musculus. 9 samples. Type: Expression profiling by high throughput sequencing.
Single-cell and single-nucleus transcriptome analysis of pattern formation in the early embryo of the spider Parasteatoda tepidariorum
GEO Series GSE201705. Parasteatoda tepidariorum. 3 samples. Type: Expression profiling by high throughput sequencing.
Integrative Proteome, Transcriptome and DNA Methylome Analysis of Regulatory Networks During U937-derived Macrophage Polarization from an M2 to M1 Phenotype [array]
GEO Series GSE127981. Homo sapiens. 6 samples. Type: Expression profiling by array; Non-coding RNA profiling by array.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.