This page contains additional data supporting our manuscript

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq
Amit Zeisel, Ana B. Muñoz Manchado, Peter Lönnerberg, Gioele La Manno, Simone Codeluppi, Anna Juréus, Sueli Marques, Hermany Munguba, Liqun He, Christer Betsholtz, Charlotte Rolny, Gonçalo Castelo-Branco, Jens Hjerling-Leffler and Sten Linnarsson

Published in Science (2015)

Looking for data on perivascular macrophages? Look here.


  • The expression heatmap showing genes and cells sorted and grouped into nine clusters using the BackSPIN algorithm.

  • Browse the genome to explore the aligned data by major cell class. Vertical scale is log(molecules/cell + 1) and tracks are colored as in Fig. 1. Pay attention to the vertical scale - you may need to adjust it to see anything.

Download raw data:

  • Cell images (very large PDF) in heatmap order.

  • Expression barplots (very large PDF) in heatmap order and in absolute units of molecules per cell. Each barplot corresponds to a single pixel row in the expression heatmap.

  • Raw data for mRNA, expressed repeats, mitochondrial genes and ERCC Spike-Ins. Tab-delimited text files with columns in heatmap order (for mRNA, column 2 indicates group assignment of genes in the level 1 BackSPIN analysis).