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8,071
datasets available to search
ShareScore release 0.9.0
Dataset results
8,071 results for “transcriptome analysis”
Transcriptome analysis of developing mammalian postnatal intestinal crypts and villi
GEO Series GSE109054. Mus musculus. 23 samples. Type: Expression profiling by high throughput sequencing.
Differential gene expression analysis by assessing transcriptome-wide expression variation between tissue specimen of prostate cancer (PCa) and benign prostate hyperplasia (BPH)
GEO Series GSE134073. Homo sapiens. 64 samples. Type: Expression profiling by high throughput sequencing.
Uniform approach for pathway and gene-set based analysis of heterogeneity in single-cell epigenome and transcriptome profiles
GEO Series GSE156138. Homo sapiens. 162 samples. Type: Expression profiling by high throughput sequencing.
Transcriptomic analysis of normal and Ino-RNA treated cells.
GEO Series GSE20936. Homo sapiens. 12 samples. Type: Expression profiling by array.
Single cell transcriptome analysis identified a unique neutrophil type associated with Alzheimer’s Disease
GEO Series GSE255662. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
Transcriptome analysis of LPS-stimulated BMDMs pretreated with Ctrl MO or Regnase-1-targeting MOs (Reg1-MOs)
GEO Series GSE182641. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
Next Generation Sequencing Analysis of Mycfl/fl and MycΔIE, ERT2 intestinal transcriptomes
GEO Series GSE155460. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Transcriptome analysis of Katnal2 knock-out mutant and wild-type mice
GEO Series GSE219228. Mus musculus. 20 samples. Type: Expression profiling by high throughput sequencing.
Transcriptomic analysis of blastocyst according to peripubertal age of bull (10 vs 16 months)
GEO Series GSE128355. Bos taurus. 4 samples. Type: Expression profiling by array.
small RNA-seq analysis of transcriptomes at 5 day after sexual induction in Fusarium graminearum strains
GEO Series GSE87835. Fusarium graminearum. 7 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Transcriptome analysis of hiPSC derived lt-NES cells
GEO Series GSE225719. Homo sapiens. 4 samples. Type: Expression profiling by array.
Transcriptomics analysis of neurogenesis by striatal astrocytes upon Rbpj-K deletion
GEO Series GSE153916. Mus musculus. 1 samples. Type: Expression profiling by high throughput sequencing.
Transcriptome analysis of cardiac organoids derived from Duchenne Muscular Dystrophy patient-derived inudced pluripotent stem cells
GEO Series GSE194297. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Single-cell transcriptomic analysis of mouse lung CD11b+ dendritic cells post allergic sensitization
GEO Series GSE156527. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
Next Generation sequencing and quantitative transcriptomic analysis in -77+/+ and -77-/- erythroid precursors
GEO Series GSE96059. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Meta-Analysis of the transcriptomic profile of human placenta
<p>The establishment of a complex multi-scale model of biological tissue is of great significance for the study of related diseases, and the integration of relevant quantitative data is the premise to achieve this goal. Whereas, the systematic collation of data sets related to placental tissue is relatively lacking. In this study, 18 published transcriptomes (a total of 425 samples) datasets of human pregnancy-related tissues (including chorionic villus and decidua, term placenta, endometrium, in vitro cell lines, etc.) from public databases were collected and analyzed. We compared the most widely used dimensionality reduction (DR) methods to generate a 2D-map for visualization of these data. We also compared the effects of different parameter settings and commonly used manifold learning methods on the results. The result indicates that the nonlinear method can better preserve the small differences between different subtypes of placental tissue than the linear method. It led the foundation for the study on accurate computational modeling of placental tissue development in the future. The datasets and analysis provide a useful source for the researchers in the field of the maternal-fetal interface and the establishment of pregnancy.</p>
Cytosplore-Transcriptomics: a scalable inter-active framework for single-cell RNA sequenc-ing data analysis
<p>Allen institute 10X mouse data (<a href="https://portal.brain-map.org/atlases-and-data/rnaseq/mouse-whole-cortex-and-hippocampus-10x">https://portal.brain-map.org/atlases-and-data/rnaseq/mouse-whole-cortex-and-hippocampus-10x</a>) converted into h5 format including metadata, to be easily uploaded in Cytosplore-Transcriptomics.</p>
Data from: Comprehensive transcriptome analysis of Crocus sativus for discovery and expression of genes involved in apocarotenoid biosynthesis
Background: Crocus sativus stigmas form rich source of apocarotenoids like crocin, picrocrocin and saffranal which besides imparting color, flavour and aroma to saffron spice also have tremendous pharmacological properties. Inspite of their importance, the biosynthetic pathway of Crocus apocarotenoids is not fully elucidated. Moreover, the mechanism of their stigma specific accumulation remains unknown. Therefore, deep transcriptome sequencing of Crocus stigma and rest of the flower tissue was done to identify the genes and transcriptional regulators involved in the biosynthesis of these compounds. Results: Transcriptome of stigma and rest of the flower tissue was sequenced using Illumina Genome Analyzer IIx platform which generated 64,604,402 flower and 51,350,714 stigma reads. Sequences were assembled de novo using trinity resulting in 64,438 transcripts which were classified into 32,204 unigenes comprising of 9853 clusters and 22,351 singletons. A comprehensive functional annotation and gene ontology (GO) analysis was carried out. 58.5 % of the transcripts showed similarity to sequences present in public databases while rest could be specific to Crocus. 5789 transcripts showed similarity to transcription factors representing 76 families out of which Myb family was most abundant. Many genes involved in carotenoid/apocarotenoid pathway were identified for the first time in this study which includes zeta-carotene isomerase and desaturase, carotenoid isomerase and lycopene epsilon-cyclase. GO analysis showed that the predominant classes in biological process category include metabolic process followed by cellular process and primary metabolic process. KEGG mapping analysis indicated that pathways involved in ribosome, carbon and starch and sucrose metabolism were highly represented. Differential expression analysis indicated that key carotenoid/apocarotenoid pathway genes including phytoene synthase, phytoene desaturase and carotenoid cleavage dioxygenase 2 are enriched in stigma thereby providing molecular proof for stigma to be the site of apocarotenoid biosynthesis. Conclusions: This data would provide a rich source for understanding the carotenoid/apocarotenoid metabolism in Crocus. The database would also help in investigating many questions related to saffron biology including flower development.
Data from: De novo transcriptome assembly and analysis of differential gene expression in response to drought in European beech
Despite the ecological and economic importance of European beech (Fagus sylvatica L.) genomic resources of this species are still limited. This hampers an understanding of the molecular basis of adaptation to stress. Since beech will most likely be threatened by the consequences of climate change, an understanding of adaptive processes to climate change-related drought stress is of major importance. Here, we used RNA-seq to provide the first drought stress-related transcriptome of beech. In a drought stress trial with beech saplings, 50 samples were taken for RNA extraction at five points in time during a soil desiccation experiment. De novo transcriptome assembly and analysis of differential gene expression revealed 44,335 contigs, and 662 differentially expressed genes between the stress and normally watered control group. Gene expression was specific to the different time points, and only five genes were significantly differentially expressed between the stress and control group on all five sampling days. GO term enrichment showed that mostly genes involved in lipid- and homeostasis-related processes were upregulated, whereas genes involved in oxidative stress response were downregulated in the stressed seedlings. This study gives first insights into the genomic drought stress response of European beech, and provides new genetic resources for adaptation research in this species.
Integrative analysis of spatial and single-cell transcriptome data from human pancreatic cancer reveals an intermediate cancer cell population associated with poor prognosis_Spatial H&E images
<p>High-resolution H&E images of spatial transcriptome data</p>
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.