Gene expression in the developing HSC niche


N.B. This site is optimised for use with Mozilla Firefox or Google Chrome web browsers

Data source

This is a the interface for our gene expression profiling of the niche for developing HSCs from the article: "A molecular roadmap of the AGM but reveals BMPER as a novel regulator of HSC maturation".

Click on a tab to select RNA-sequencing data from either the AGM regions at E9.5 and E10.5 or OP9 cells cultured in reaggregate or flat conditions.

Samples were prepared as sequencing data normalised as described in the above article.


This interface enables quick searching of datasets, simple filtering and links to external databases.

The images and filters:

  • Select a sample of interest by clicking on the interactive image.
  • Apply filters to the selected sample's expression profile using the controls on the right to select genes above a minimum RPM expression threshold, or to select genes with predicted functionality.
  • In the AGM data tab, the "cluster" panel allows selection of pre-computed gene clusters (as described in the article).
  • Additional information on filters can be found by hovering over the information icons next to each filter.

The results table:

  • All filters will be applied to the results table below, which can then be ordered by any column.
  • A particular gene of interest can be selected by typing its MGI symbol or Ensembl ID into the search box on the right.
  • For any gene of interest, access its entry in Ensembl, or in the Edinburgh Mouse Atlas project by with the buttons on the right of the data table.