Transcriptome

Description:

Using single cell transcriptomic approach from the 10X genomic platform we provide the  gene expression profiles for 2592 and 3804 individual cells from the pituitaries of female and male adult medaka (Oryzias latipes), respectively. Based on expression profile clustering, 15 and 16 distinct cell types were defined in the female and male pituitary, respectively, of which nine are involved in the exclusive production of a single peptide hormone. One cell cluster appears to be unique to the male pituitary. Collectively, our data provide a high-quality reference for studies on pituitary biology and the regulation of hormone production, both in fish and in vertebrates in general. 

How to investigate the dataset:

The main data record consists of barcodes.tsv, features.tsv and matrix.mtx files, listing raw UMI counts for each gene (feature) in each cell (barcode) in a sparse matrix format. In addition, we provide a table of cell type assignments and UMAP projections for each individual cell (barcode), as well as a summary of the top differentially expressed genes per cell type. Raw sequencing data are available in FASTQ format. Finally, the data record contains matrix files on exonic and intronic expression, which can be used for Velocyto gene expression dynamics analyses.

We then invite you to follow the tutorial made by Satijalab to start with Seurat to use our R code available  on GitHub to open and process the data set.

Published 1. May 2021 - 7:00 - Updated 1. May 2021 - 7:00