Data: Sj BulkRNA 14-28d
Raw sequencing data from Wang et al 2017 were downloaded and re-mapped to HuSjV2 genome. Normalised expression based on library-size and gene length were calculated using edgeR.
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Interactive exploration of schistosome expression data
public and re-analyzed; multi-species; at the levels of bulk, single-cell, and spatial (ITF) atlases!
Explore Schisto.xyz V2New Features
Interactive viz
(Multiple) Gene queries, flexible embeddings and metadata.
Web sharing
Share the current visualization state easily in a URL.
Smart search
Fast expression exploration in multiple datasets simultaneously.
Schisto.xyz is now more powerful and interactive.
Serving schisto researchers since 2018, now offers enhanced datasets, interactive visualisation solutions, and a re-designed powerful search engine.
Multimodal datasets
Bulk RNA-seq for all life stages; integrative re-analysis; single-cell atlases; spatial expression (ITF).
Interactive and sharable
Browser-based interactive visualisation supports multiple queries and embeddings, easy share of states via URLs.
Easy customization
Metadata selection, point colors/sizes, subsetting, distribution and composition plots, all highly customizable.
Powerful search
The search engine has been re-designed to provide an expression overview across multiple datasets, fast and robust.
Robust Search & Expression Overview
Fast visualisation of expression in millions of cells / samples, across multiple datasets, at one time.
Explore your favourite geneAtlas-level Datasets
Sj bulk RNA-seq 14-28d
Sj bulk RNA-seq data from Wang et al 2017 PMID:28287085, 48 samples 14-28dpi, re-processed
Smed scRNA all timepoints
Planarian 55K cells at different regeneration time, norm counts. PMID:37268637
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Life-cycle Timepoints
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Bulk Samples
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K Single Cells
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Spatial Sections
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Data: planarian spatial multiple sections
The study provided multiple Visium sections for Schmidtea mediterranea at 0hpa. On the scanpy data I modified the spatial coordinates for a better view, and also constructed their 3D structure.
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While the schisto.xyz database includes an original integrative analysis of bulk RNA-seq data, most datasets are collected from external studies, for which the original publications should be cited.
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Questions? Adding your data?
Feel free to drop me a message via social media / email / contact form. If you find the resource useful, please cite (for now)
Lu et al, bioRxiv 308213 (2018) https://doi.org/10.1101/308213
SchistoXYZ (schisto.xyz)