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7,327
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7,327 results for “pathways”
Data from: The impact of autotrophic versus heterotrophic nutritional pathways on colony health and wound recovery in corals
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Data from: Curcumin improves glycolipid metabolism through regulating peroxisome proliferator activated receptor γ signalling pathway in high-fat diet-induced obese mice and 3T3-L1 adipocytes
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Data from: Live, dead, and fossil mollusks in Florida freshwater springs and spring-fed rivers: taphonomic pathways and the formation of multi-sourced, time-averaged death assemblages
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Data from: Independent sources of condition dependency and multiple pathways determine a composite trait: lessons from carotenoid-based plumage colouration
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Data from: Human endometrial transcriptome and progesterone receptor cistrome reveal important pathways and epithelial regulators
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Data from: Divergent pathways of nitrogen-fixing trees through succession depend on starting nitrogen supply and priority effects
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Ancient balancing selection maintains incompatible versions of the galactose pathway in yeast (Figure creation)
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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.
Sensory neurons co-opt classical immune signaling pathways to mediate chronic itch [6 NaV1.8+ Il4raF/F mice treated with MC903 compared to skin from 4 littermates]
GEO Series GSE100397. Mus musculus. 10 samples. Type: Expression profiling by high throughput sequencing.
Discovery of new candidate genes for rheumatoid arthritis through integration of genetic association data with expression pathway analysis
GEO Series GSE90081. Homo sapiens. 24 samples. Type: Expression profiling by high throughput sequencing.
Selective and brain-penetrant lanosterol synthase inhibitors target glioma stem-like cells by activating a shunt pathway that generates the toxic metabolite 24(S),25-epoxycholesterol
GEO Series GSE222971. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
Heterogenous radiomics patterns are associated with poor survivals and dysregulated pathways in medulloblastoma
GEO Series GSE151519. Homo sapiens. 17 samples. Type: Expression profiling by high throughput sequencing.
Identify the key signaling pathway involved in the Tet2 deficiency-induced clonal hematopoiesis
GEO Series GSE232384. Mus musculus. 55 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.
Discovery of target genes and pathways of blood trait loci using pooled CRISPR screens and single cell RNA sequencing
GEO Series GSE171452. Homo sapiens. 28 samples. Type: Other.
Oxicam-type nonsteroidal anti-inflammatory drugs inhibit NPR1-mediated salicylic acid pathway
GEO Series GSE154593. Arabidopsis thaliana. 24 samples. Type: Expression profiling by high throughput sequencing.
Multiple genes recruited from hormone pathways partition maize diterpenoid defences.
GEO Series GSE120135. Zea mays. 8 samples. Type: Expression profiling by high throughput sequencing.
Plasma amino acids regulate pancreatic acinar cell proliferation and size via mTORC1 and YAP/TAZ signaling pathways
GEO Series GSE243695. Mus musculus. 9 samples. Type: Expression profiling by high throughput sequencing.
Targeted DNA methylation of the ALS/FTD gene C9orf72 via endogenous DNA damage repair pathways (II)
GEO Series GSE134995. Homo sapiens. 8 samples. Type: Methylation profiling by genome tiling array.
Single cell evaluation of endocardial HAND2 gene regulatory networks reveals critical HAND2 dependent pathways impacting cardiac morphogenesis.
GEO Series GSE210221. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
ScienceDex guides
Understand access before you commit
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.