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Single cell transcriptomic profiling

You can download processed RNA sequencing data for mouse cells and human nuclei from the RNA Seq page. You can also download from that page the reference genomes (.gtf files) used to align the raw data. For information on the methods used to obtain the data see the whitepapers located in Documentation.

The sampled brain regions and the number of samples are listed below. The data for each brain region is provided in a zip file containing the numerical data in matrix form, and separate csv files with information on the individual samples (columns) and genes (rows) in the reference genome used. Details are provided in a README.txt file. 

For a subset of the transcriptomics data, you can visualize and explore gene expression by means of a Heatmap Viewer. This sub-set consists of 1,772 mouse cells from the dorsal part of the lateral geniculate complex (LGd). 

To launch the Heatmap Viewer, go to the Download page and click the "RNA-Seq heatmap for LGd" link in the table listing the available data. For more information on how to use the Heatmap Viewer click here.

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