Transcriptomic analysis of CA1 inhibitory interneurons

Here you find transcriptomic data of CA1 GABAergic neurons, together with analysis results described in the paper "Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics" by Kenneth D. Harris, Hannah Hochgerner, Nathan G. Skene, Lorenza Magno, Linda Katona, Carolina Bengtsson Gonzales, Peter Lonnerberg, Peter Somogyi, Nicoletta Kessaris, Sten Linnarsson, and Jens Hjerling-Leffler (

The file CA1Interneurons.mat contains all data in a MATLAB structure; a suite of MATLAB functions for plotting and processing this data can be found at

The remaining files contain the same data in tab separated text format.

The file expression.tsv contains the UMI gene counts. Each column in the file corresponds to a cell. The first row contains the "cell name" - an actual name randomly assigned to each cell from a list of baby names released by the US census bureau. This name serves as a human-memorable unique identifier for each cell. Each row after that lists the expression of all genes in the cells, with the gene name in the first column.

The file analysis_results.tsv contains the results of ProMMT cluster analysis, nbtSNE, and latent factor analysis (described in the manuscript) in a similar format.

The file cell_metadata.tsv contains miscellaneous information from the sequencing pipeline again in the same format.

The file latent_weights.tsv contains the gene weights coming from the latent factor analysis, in a similar format but now with a column for each gene that entered into this analysis (which is not all of them)

For more files, including the raw sequencing data, please go to

For questions or correspondence please email