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2,614 results for “RNA-seq analysis”
Data from: Understanding the genomic basis of adaptive response to variable osmotic niches in freshwater prawns: a comparative intraspecific RNA-Seq analysis of Macrobrachium australiense
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Data from: Identification of immunity-related genes in Dialeurodes citri against entomopathogenic fungus Lecanicillium attenuatum by RNA-seq analysis
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Data from: Whole transcriptome RNA-Seq analysis of breast cancer recurrence risk using formalin-fixed paraffin-embedded tumor tissue
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RNA-seq analysis reveals the role of Omp16 during Brucella infected RAW264.7 cells
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Comparative gene expression analysis in the Arabidopsis thaliana root apex using RNA-seq and microarray transcriptome profiles
The root apex is an important section of the plant root involved in environmental sensing and cellular development. Analyzing the gene profile of root apex in diverse environments is important and challenging especially when the samples are limiting and precious such as in spaceflight. The feasibility of using tiny root sections for transcriptome analysis was examined in this study. To understand the gene expression profiles of the root apex Arabidopsis thaliana Col-0 roots were sectioned into Zone-I (0.5 mm root cap and meristematic zone) and Zone-II (1.5 mm transition elongation and growth terminating zone). Gene expression was analyzed using microarray and RNA seq. Both the techniques arrays and RNA-Seq identified 4180 common genes as differentially expressed (with > two-fold changes) between the zones. In addition 771 unique genes and 19 novel TARs were identified by RNA-Seq as differentially expressed which were not detected in the arrays. Single root tip zones can be used for full transcriptome analysis; further the root apex zones are functionally very distinct from each other. RNA-Seq provided novel information about the transcripts compared to the arrays. These data will help optimize transcriptome techniques for dealing with small rare samples.
Efficient Identification of Multiple Pathways: RNA-Seq Analysis of Livers from 56Fe Ion Irradiated Mice
Background: mRNA interactions with each other and other signaling molecules define different biological pathways and functions. Researchers have been investigating various tools to analyze these types of interactions. In particular gene co-expression network methods have proved useful in finding and analyzing these molecular interactions. Many different analytical pipelines to identify these interactions networks have been proposed with the aim of identifying an optimal partition of the network where the individual modules are neither too small to make any general inference or too large to be biologically interpretable. Results: In this study we propose a new pipeline to perform gene co-expression network analysis. The proposed pipeline uses WGCNA a widely used software to perform different aspects of gene co-expression network analysis and modularity maximization algorithm to analyze novel RNA-Seq data to understand the effects of low-dose 56Fe ion irradiation on the formation of hepatocellular carcinoma in mice. The network results along with experimental validation show that using WGCNA combined with Modularity provide a more biologically interpretable network in our dataset. Our pipeline showed better performance than the existing clustering algorithm in WGCNA in finding modules and identified a module with mitochondrial subunits that are supported by mitochondrial complex assay. Conclusions: We present a pipeline that can reduce the problem of parameter selection with the existing algorithm in WGCNA for comparable RNA-Seq datasets which may assist in future research to discover novel mRNA interactions and their downstream molecular effects. C57BL16 males were placed into 2 treatment groups and received the following irradiation treatments at Brookhaven National Laboratories (Long Island NY): 600 MeV/n 56Fe (0.2 Gy) and no irradiation. Left liver lobes were collected at 30 60 120 270 and 360 days post-irradiation flash frozen and stored at -80 xc2 xb0C until they could be processed for RNA-Seq. Livers were sampled by taking two 40-micron thick slices using a cryotome at -20 xc2 xb0C. This allowed multiple sampling of the tissue without the tissue going through multiple freeze/thaw cycles. Total RNA was isolated from the liver slices using RNAqueousTM Total RNA Isolation Kit (ThermoFisher Scientific Waltham MA) and rRNA was removed via Ribo-ZeroTM rRNA Removal Kit (Illumina San Diego CA) prior to library preparation with the Illumina TruSeq RNA Library kit. Samples were sequenced in a paired-end 50 base format on an Illumina HiSeq 1500. Reads were aligned to the mouse GRCm38 reference genome using the STAR alignment program version 2.5.3a with the recommended ENCODE options. The -quantMode GeneCounts option was used to obtain read counts per gene based on the Gencode release M14 annotation file. Total number of reads used in analysis varies between 23-35 millions of reads.
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.
Gene Expression Analysis of Cancer-Associated Fibroblast (CAF) compared to Normal Fibroblast (NF) [RNA-seq]
GEO Series GSE55870. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
RNA-seq analysis of proximal tubule specific Fan1 knockout transgenic kidneys subjected to cisplatin injury
GEO Series GSE163862. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
RNA-seq analysis of alleles of the atrR transcription factor-encoding gene in Aspergillus fumigatus
GEO Series GSE123445. Aspergillus fumigatus Af293. 8 samples. Type: Expression profiling by high throughput sequencing.
RNA-seq Analysis of 14-day-old WT, bcl7a(brip3), bcl7b(brip4), bcl7a bcl7b(brip3 brip4), bcl7a bcl7b brm-3(brip3 brip4 brm-3) and bcl7a bcl7b brm-1(brip3 brip4 brm-1) seedlings under short day conditi
GEO Series GSE215151. Arabidopsis thaliana. 24 samples. Type: Expression profiling by high throughput sequencing.
RNA-Seq analysis of wild-type and ttpA-C231S, ttpA-E236fsx, and ttpA-Y242fsx mutant D. discoideum amebae
GEO Series GSE156809. Dictyostelium discoideum. 16 samples. Type: Expression profiling by high throughput sequencing.
RNA-Seq analysis comparing p53-null versus ΔNp63Δ/Δ;p53-null or ΔNp73Δ/Δ;p53-null thymic lymphoma tumors
GEO Series GSE60827. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
Transcriptomic analysis (RNA-seq) of early iPSC-CMs between PA-IVS and healthy control.
GEO Series GSE233349. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
RNA-seq analysis asociated with the infection of bovine papillomavirus
GEO Series GSE122853. Bos taurus. 6 samples. Type: Expression profiling by high throughput sequencing.
Integrative analysis of DNA methylation and microRNA expression reveals mechanisms of disparity in hepatocellular carcinoma [RNA-Seq]
GEO Series GSE176271. Homo sapiens. 32 samples. Type: Expression profiling by high throughput sequencing.
Molecular and spatial analysis unveils the functional basis of tertiary lymphoid structures in Sjogren’s syndrome[bulk RNA-seq]
GEO Series GSE272410. Homo sapiens. 73 samples. Type: Expression profiling by high throughput sequencing.
RNA-seq analysis of gene expression in the liver of control and Mst1/2 deficient mice
GEO Series GSE95463. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Transcriptome profiles of mouse embryonic stem cells cultured in different conditions by RNA-seq analysis
GEO Series GSE109418. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
RNA-Seq analysis of the WEHI-231-derived stable cell lines WEHI-control and WEHI-miR-148a
GEO Series GSE75809. Mus musculus. 8 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.