zglu

About author

Intro

Zhigang is a computational biologist interested in gene expression and regulation, functional genomics, and drug targets discovery. He works on multi-layered omics data (genomics, transcriptomics, epigenomics, single-cell and spatial transcriptomics), applys machine learning modelling and does large-scale dataset visualisation (eg. web-sharing).

He has knowledge and years of experience in NGS, single-cell and spatial multi-omics, bioinformatics, parasite biology and oncology.

Author's posts

Data: Sm miracidium and sporocyst scRNA-seq

Single-cell datasets for S. mansoni miracidia (20K cells) and D5 sporocysts (601 cells) are available now!

Data: Sj bulkRNA larval stages

S. japonicum bulk RNA-seq covering larval stages from Cheng et al 2022. Data was mapped to the HuSjv3 genome and TPM was used for normalization.

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.

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.

How to Cite

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.

Data: Integrative Bulk All Life Stages

The analysis was performed before: https://v7test.schisto.xyz/dataused/ where 186 bulk sample data from 6 projects were processed with mapping and count.

Previous links

As the structure of schisto.xyz has been largely re-designed, data of previous versions are still accessable using the original URLs.

Genesets between Sm v7 and v10

While there is a hugo improvement in the genome assembly from V7 to V10, the geneset stays largely the same.

Data: Sm Adult scRNA-seq

The processed data (a Seurat object) was downloaded from Wendt et al 2020 Science paper and I did some modifications.