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Transcriptomic analysis of CA1 inhibitory interneurons

dataset
posted on 28.04.2018, 23:54 by Kenneth Harris, Hannah Hochgerner, Nathan G. Skene, Lorenza Magno, Linda Katona, Carolina Bengtsson Gonzales, Peter Lonnerberg, Nicoletta Kessaris, Sten Linnarsson, Jens Hjerling-Leffler
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 (https://www.biorxiv.org/content/early/2018/04/18/143354)

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 https://github.com/cortex-lab/Transcriptomics.

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 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE99888

For questions or correspondence please email kenneth.harris@ucl.ac.uk

Funding

Wellcome Trust (108726 to KDH, NK, PS, SL, and JH-L), Medical Research Council (PS) European Research Council (261063 to SL), Swedish Research Council (STARGET to SL, and 2014-3863 to JH-L), StratNeuro (JH-L), Knut and Alice Wallenberg Foundation (SL) and European Union FP7/Marie Curie Actions (322304 to JH-L)

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