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Dataset results
2,614 results for “RNA-seq analysis”
Multi-omics analysis in primary T cells elucidates mechanisms behind disease associated genetic loci [RNA-seq]
GEO Series GSE282511. Homo sapiens. 128 samples. Type: Expression profiling by high throughput sequencing.
RNA-seq analysis of mycobacteria stress response to microgravity
The aim of this work is to determine whether mycobacteria have enhanced virulence during space travel and what mechanisms they use to adapt to microgravity. M. marinum and LHM4 were grown in high aspect ratio vessels (HARV) in a rotary cell culture system (RCCS) under normal gravity (NG) or low shear simulated microgravity (MG). To determine the effect of MG on the stress responses activated by the growth conditions, we used RNAseq to examine what genes were expressed. For RNAseq, the bacteria are harvested, RNA isolated and converted DNA (cDNA), and the cDNA sequenced. Using bioinformatics, the amount of expression of the different M. marinum genes were compared between the NG and MG samples. To make sure that we were examining only gene expression changes due to MG, only bacteria in early exponential growth were used in the RNAseq studies. Triplicate NG and MG cultures were used to generate samples of bacteria grown for ~40 hrs. We also grew triplicate cultures for 4 days and then diluted them again and grew them for another ~40 hrs so we could examine gene expression from bacteria exposed for a longer time. In summary, this study determined that waterborne mycobacteria alter their growth, expression of stress responses, and their sensitivity to oxidizing conditions when subjected to growth under MG.
RNA-Seq analysis identifies potential modulators of gravity response in Ceratopteris spores: Evidence for modulation by calcium pumps and apyrase activity
Gravity regulates the magnitude and direction of a trans-cell calcium current in germinating spores of Ceratopteris richardii. Blocking this current with nifedipine blocks the spore's downward polarity alignment, a polarization that is fixed by gravity 10 h after light induces the spores to germinate. RNA-seq analysis at 10 h was used to identify genes potentially important for the gravity response. The data set will be valuable for other developmental and phylogenetic studies.
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.
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.
RNA-Seq analysis of cancer models with altered SLX4/XPF reveals links to migration, DNA damage response, EMT, and drug sensitivity
GEO Series GSE309364. Homo sapiens. 60 samples. Type: Expression profiling by high throughput sequencing.
Single-Cell RNA-Seq Analysis of long-term transplanted single-cell-derived mouse DASC in host lung
GEO Series GSE168573. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
Hepatocyte RNA-seq analysis in liver-specific XBP1 knockout mice fed a high fat sugar diet
GEO Series GSE190947. Mus musculus. 11 samples. Type: Expression profiling by high throughput sequencing.
Dual RNA-seq analysis unveils Trichoderma NoxR as an essential mediator of the molecular dialogue during interaction with Arabidopsis
GEO Series GSE138203. Trichoderma atroviride; Arabidopsis thaliana. 29 samples. Type: Expression profiling by high throughput sequencing.
RNA-seq analysis of grape-like organoids and others in iPSC derived Hepatocyte organoids (iHOs)
GEO Series GSE285436. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
RNA-seq analysis of primary dermal fibroblasts of Hutchinson-Gilford progeria syndrome.
GEO Series GSE141950. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
RNA-Seq analysis of Gtf2ird1 knockout epidermal tissue provides potential insights into molecular mechanisms underpinning Williams-Beuren syndrome
GEO Series GSE81082. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
RNA-seq analysis of HT8 cells based on PPDPF knockdown
GEO Series GSE173575. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
Digital RNA-Seq for transcriptome analysis in splenic human CD4-positive T cells of mock-infected humanized mice and GFP-positive and GFP-negative CD4-positive cells of HIV1-GFP-infected humanized mic
GEO Series GSE137644. Homo sapiens. 37 samples. Type: Expression profiling by high throughput sequencing.
RNA-seq Analysis of BMDM treated with cancer-cell conditioned medium in the presence or abscence of lipid contents
GEO Series GSE166735. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
RNA-Seq analysis of Pold3 inducible-knockout embryonic stem cells
GEO Series GSE100945. Mus musculus. 3 samples. Type: Expression profiling by high throughput sequencing.
RNA-Seq analysis of roots of Axonopus compressus in response to aluminum toxicity
GEO Series GSE254750. Axonopus compressus. 6 samples. Type: Expression profiling by high throughput sequencing.
Liver transcriptome analysis of the large yellow croaker under fasting or temperature treatment by RNA-seq
GEO Series GSE67756. Larimichthys crocea. 4 samples. Type: Expression profiling by high throughput sequencing.
Transcriptomic analysis of sorted lung cells revealed a proviral activity of the NF-κB pathway towards SARS-CoV-2 (RNA-Seq depleted polyA)
GEO Series GSE244484. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
Comparative transcriptome analysis of two cotton speices by RNA-seq
GEO Series GSE109782. Gossypium hirsutum. 2 samples. Type: Expression profiling by high throughput sequencing.
ScienceDex guides
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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.