In silico Transcriptome (iTranscriptome)

Geo-sequencing: 3D Transcriptome of mouse embryo at gastrulation

About iTranscriptome

iTranscriptome is the 3D gene expression database of gastrulating mouse embryo (~ E6.5 - E7.5).

The current version of the database is built from expression data collated from one C57BL/6 embryo at mid-gastrulation (~E7.0, late mid-streak stage (Kojima et al., 2014)). The embryo was serially cryo-sectioned in the plane transverse to the proximal-distal axis. From a total of 22 sections, cells were sampled from 11 alternating sections. On each section, approximately 20 cells were isolated by laser capture microdissection from the epiblast in each of the quadrants: anterior (A), posterior (P) and left lateral (L) and right lateral (R), except for the distal-most section where only anterior and posterior halves were sampled. Altogether, 42 cell samples with spatial coordinate information (e.g., 3A, 4P, 5R, 6L etc with section 1 being the most distal) were collected for RNA isolation. RNA-sequencing was performed using a modified single-cell based low-input sequencing method. In addition, two embryos at the same developmental stage (the testers) were analysed in parallel to generate data for verifying the consistency of the spatial transcriptome of the reference embryo. Further information on data analysis is presented in the paper.

Features of iTranscriptome

The sequencing data with spatial information cover over 20,000 genes that are expressed in the epiblast of the gastrulating mouse embryo. The data are collated into a high-resolution 3D transcriptome - the iTransctiptome. 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 and expressing in one of the 20 stereotypic patterns depicted in the in-built templates and calculate the corraliton between all samples in reference embryo and query trancriptome data.

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

Long-term Goal

Work is in progress to collate the iTranscriptome of embryos at other stages of gastrulation. Our goal is to document a complete iTranscriptome of mouse gastrulaton.


Guangdun Peng, Shengbao Suo, Jun Chen, Weiyang Chen, Chang Liu, Fang Yu, Ran Wang, Shirui Chen, Na Sun, Guizhong Cui, Lu Song, Patrick P.L. Tam, Jing-Dong J. Han, Naihe Jing. Spatial Transcriptome for the Molecular Annotation of Lineage Fates and Cell Identity in Mid-gastrula Mouse Embryo. Developmental Cell, 2016 Mar. 36: 681-697.

 Jun Chen, Shengbao Suo, Patrick PL Tam, Jing-Dong J. Han, Guangdun Peng, Naihe Jing. Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq. Nature Protocols, 2017 Feb. 12: 566-580.


Key features

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


  • - More sensitive
  • - Searchable web service

Accessing iTranscriptome

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 20 predefined patterns).
Zipcode Mapping
Identifying potential regions in the reference embryo from which a sample is derived based on sample’s transcriptome data.