In silico Transcriptome (iCHTatlas)

ICHTatlas: Multi-demensional Transcriptome of zebrafish at CHT region

About iCHTatlas

iCHTatlas is the 3D gene expression, bulk RNA-seq and single-cell RNA-seq database of HSCs progression in zebrafish CHT region.

Here, we use multi-dimension approaches including bulk RNA-seq, GEO-seq and single cell RNA-seq to characterize the detailed spatial-temporal transcriptomics during HSPC expansion and differentiation in the CHT of zebrafish. Combinatorial expression profiling reveal that in the CHT niche, HSPCs and neighboring supporting cells are regulated by shared signaling pathways and intrinsic factors, such as integrin signaling and smchd1. Unexpectedly, live imaging together with scRNA-seq demonstrates that de novo HSPC emergence occurs in the CHT through endothelial-to-hematopoietic transition (EHT). Interestingly, scRNA-seq analysis unveils the strong correlation between cell cycle and HSPC differentiation. Taken together, our results provide a global transcriptome landscape for an intact hematopoietic organ in which HSPCs rapidly expand/differentiate and that the key signaling and factors revealed here will provide useful insights for expansion of HSPCs in vitro or ex vivo.


Features of iCHTatlas

The sequencing data with spatial time-series and high-resolution transcriptome cover over 20,000 genes that are expressed in the CHT region in zebrafish during HSCs expansion. The data are collated into a comprehensive 3D transcriptome - the iCHTatlas. The spatially rendered gene expression data are displayed in the 2D format (the corn plot) and in the 3D format on a digital embryo template (digital whole mount in situ hybridization, d-WISH). The database can be mined to show gene's expresson pattern, identify genes showing similar spatial pattern of expression.

Corn plot visualization and zip-code mapping utilities can be downloaded from here.

Long-term Goal


Yuanyuan Xue#, Denghui Liu#,Guizhong Cui, Yanyan Ding, Daosheng Ai, Suwei Gao, Yifan Zhang, Shengbao Suo, Xiaohan Wang, Peng Lv, Chunyu Zhou, Yizhou Li, Xingwei Chen, Guangdun Peng, Naihe Jing, Jing-Dong J. Han*, Feng Liu*. Multi-dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion. Journal, 2019 r. 36: 681-697.


Key features

  • - High resolution
  • - 2D & 3D visualization


  • - More sensitive
  • - Searchable web service

Accessing iCHTatlas

Pattern search by gene
Querying and displaying the expression pattern of a query gene in either a corn plot or a 3D embryo model
Gene search by gene
Searching for genes that share similar expression patterns of a query gene.
Gene search by pattern
Searching for genes using a query pattern (There are 7 predefined patterns).
Zipcode Mapping
Identifying potential regions in the reference embryo from which a sample is derived based on sample’s transcriptome data.